Index:src/fmri/polyt.c
21c21
< static char rcsid[] = "$Id: polyt.c,v 1.2 1997/11/13 23:43:08 welling Exp $";
---
> static char rcsid[] = "$Id: polyt.c,v 1.3 1998/12/03 00:24:03 welling Exp $";
60a61
>     static float sigma_dist; /* square root of variance reqmin, plus scale */
141a143,145
>     /* Construct population std deviation for use in T tests */
>     sigma_dist= (float)sqrt((*reqmin)/((float)(*n)));
> 
386c390
< 	if ((z<*ynewl) && TTEST(z,dsum,*reqmin,*tcritsqr)) {
---
> 	if ((z<*ynewl) && TTEST(z,dsum,sigma_dist,*tcritsqr)) {
392c396
< 	if ((z<*ynewl) && TTEST(z,dsum,*reqmin,*tcritsqr)) {
---
> 	if ((z<*ynewl) && TTEST(z,dsum,sigma_dist,*tcritsqr)) {
Index:src/brain/lbfgs.c
964c964
<     d_1 = abs(fold), d_2 = abs(*f), d_1 = max(d_2,d_1);
---
>     d_1 = fabs(fold), d_2 = fabs(*f), d_1 = max(d_2,d_1);
1578c1578
< 		if (abs(neggi) <= 0.) {
---
> 		if (fabs(neggi) <= 0.) {
1621c1621
< 		if (abs(neggi) > 0.) {
---
> 		if (fabs(neggi) > 0.) {
3306c3306
< 	d_1 = *sbgnrm, d_2 = abs(gi);
---
> 	d_1 = *sbgnrm, d_2 = fabs(gi);
3689c3689
<     if (*f <= ftest && abs(*g) <= *gtol * (-ginit)) {
---
>     if (*f <= ftest && fabs(*g) <= *gtol * (-ginit)) {
3725c3725
< 	if ((d_1 = sty - stx, abs(d_1)) >= width1 * .66) {
---
> 	if ((d_1 = sty - stx, fabs(d_1)) >= width1 * .66) {
3729c3729
< 	width = (d_1 = sty - stx, abs(d_1));
---
> 	width = (d_1 = sty - stx, fabs(d_1));
3884c3884
<     sgnd = *dp * (*dx / abs(*dx));
---
>     sgnd = *dp * (*dx / fabs(*dx));
3892c3892
< 	d_1 = abs(theta), d_2 = abs(*dx), d_1 = max(d_2,d_1), d_2 = abs(*dp);
---
> 	d_1 = fabs(theta), d_2 = fabs(*dx), d_1 = max(d_2,d_1), d_2 = fabs(*dp);
3906c3906
< 	if ((d_1 = stpc - *stx, abs(d_1)) < (d_2 = stpq - *stx, abs(d_2))) {
---
> 	if ((d_1 = stpc - *stx, fabs(d_1)) < (d_2 = stpq - *stx, fabs(d_2))) {
3922c3922
< 	d_1 = abs(theta), d_2 = abs(*dx), d_1 = max(d_2,d_1), d_2 = abs(*dp);
---
> 	d_1 = fabs(theta), d_2 = fabs(*dx), d_1 = max(d_2,d_1), d_2 = fabs(*dp);
3935c3935
< 	if ((d_1 = stpc - *stp, abs(d_1)) > (d_2 = stpq - *stp, abs(d_2))) {
---
> 	if ((d_1 = stpc - *stp, fabs(d_1)) > (d_2 = stpq - *stp, fabs(d_2))) {
3944c3944
<     } else if (abs(*dp) < abs(*dx)) {
---
>     } else if (fabs(*dp) < fabs(*dx)) {
3954c3954
< 	d_1 = abs(theta), d_2 = abs(*dx), d_1 = max(d_2,d_1), d_2 = abs(*dp);
---
> 	d_1 = fabs(theta), d_2 = fabs(*dx), d_1 = max(d_2,d_1), d_2 = fabs(*dp);
3984c3984
< 	    if ((d_1 = stpc - *stp, abs(d_1)) < (d_2 = stpq - *stp, abs(d_2)))
---
> 	    if ((d_1 = stpc - *stp, fabs(d_1)) < (d_2 = stpq - *stp, fabs(d_2)))
4005c4005
< 	    if ((d_1 = stpc - *stp, abs(d_1)) > (d_2 = stpq - *stp, abs(d_2)))
---
> 	    if ((d_1 = stpc - *stp, fabs(d_1)) > (d_2 = stpq - *stp, fabs(d_2)))
4023c4023
< 	    d_1 = abs(theta), d_2 = abs(*dy), d_1 = max(d_2,d_1), d_2 = abs(*
---
> 	    d_1 = fabs(theta), d_2 = fabs(*dy), d_1 = max(d_2,d_1), d_2 = fabs(*
4147c4147
< 	d_2 = scale, d_3 = (d_1 = x[i], abs(d_1));
---
> 	d_2 = scale, d_3 = (d_1 = x[i], fabs(d_1));
Index:src/mri_anova/mri_anova.c
62c62
< static char rcsid[] = "$Id: mri_anova.c,v 1.6 1998/09/01 17:59:43 welling Exp $";
---
> static char rcsid[] = "$Id: mri_anova.c,v 1.7 1998/11/06 23:44:27 welling Exp $";
94a95
> static OutFileStruct* mse_out= NULL;
113c114
< static void init_out_table( MRI_Dataset* in, int tblsize )
---
> static void init_out_table( MRI_Dataset* in, int tblsize, int mse_flag )
162a164,176
> 
>   /* If mse_flag is set, set up an output structure for MSE info */
>   if (mse_flag) {
>     if (!(mse_out= (OutFileStruct*)malloc(sizeof(OutFileStruct))))
>       Abort("%s: unable to allocate %d bytes!\n",
> 	    progname, sizeof(OutFileStruct));
>     mse_out->source= "MSE";
>     if (!(mse_out->chunk= (float*)malloc(CHUNKSIZE*sizeof(float))))
>       Abort("%s: unable to allocate %d floats!\n",progname,CHUNKSIZE);
>     mse_out->chunk_offset= 0;
>     mse_out->file_offset= 0;
>     mse_out->dset= mri_copy_dataset( "MSE", out_table[0].dset );
>   }
178a193,200
>   if (mse_out) {
>     if (mse_out->chunk_offset) {
>       mri_set_chunk(mse_out->dset, "images", mse_out->chunk_offset,
> 		    mse_out->file_offset, MRI_FLOAT, mse_out->chunk);
>       mse_out->file_offset += mse_out->chunk_offset;
>       mse_out->chunk_offset= 0;
>     }
>   }
192a215,220
>   if (mse_out) {
>     mri_close_dataset(mse_out->dset);
>     free(mse_out->source);
>     free(mse_out->chunk);
>   }
> 
478a507,510
>     if (mse_out) {
>       mse_out->chunk[mse_out->chunk_offset]= 0.0;
>       mse_out->chunk_offset++;
>     }
497a530,533
>     if (mse_out) {
>       mse_out->chunk[mse_out->chunk_offset]= sse/(float)sse_df;
>       mse_out->chunk_offset++;
>     }
528a565
>   int mse_flag= 0;
551a589
>   mse_flag= cl_present("mse");
678c716
< 	init_out_table( Input, nsources );
---
> 	init_out_table( Input, nsources, mse_flag );
Index:src/mri_anova/mri_anova_help.help
9c9
<     mri_anova [-v i j k ] [-split splitfile] [-cond confile] infile
---
>     mri_anova [-v i j k ] [-mse] [-split splitfile] [-cond confile] infile
18a19,20
>   -mse      causes a dataset to be written containing the MSE of
>             the fit.  (This option has no effect if -v is specified)
Index:src/csh/FIASCO
22c22
< echo '$Id: FIASCO,v 1.11 1998/08/28 19:28:22 welling Exp $'\
---
> echo '$Id: FIASCO,v 1.12 1998/12/03 00:30:19 welling Exp $'\
29c29
< setenv FIASCO_PATCHLVL 0
---
> setenv FIASCO_PATCHLVL 1