Greg,

Yes, your suggested fix to recon-all.makefile for the brain.mgz target is correct, and the fix will appear in the next stable release.

Note that the recon-all makefile feature has a big shortcoming that has kept me from announcing its usage publicly, and that is that it doesn't account for manually created control points or manually specified seed points (the macros CP, SEED_PONS, SEED_CC, SEED_LH and SEED_RH in the recon-all.makefile). If someone were to create control points (for instance to fix a white-matter problem), then 'recon-all -make all' will not detect this. I haven't figured-out a clever (non-hacky) way to account for these, since the default stream is not dependent on control or seed points.

Nick

On Wed, 2007-08-29 at 12:45 -0500, Greg Harris wrote:

Hi, Doug,

Thank you; I guess we'll wait a week.

Greg

On 8/29/07 12:38 PM, "Doug Greve" greve@nmr.mgh.harvard.edu wrote:

...

Hi Greg,

Nick programmed all the makefile stuff, so we'll have to wait until his return next week to get this resolved. Can you use the traditional flags?

doug

Greg Harris wrote:

...

Dear FreeSurfers,

I am trying to be a user of 'recon-all -make all'. The method stops when it attempts the step 'recon-all -s $(subj) -hemi lh -finalsurfs'. The problem at that point is that the file mri/brain.finalsurfs.mgz does not exist. The command to create this file, the only possible command if we go through rec on-all, is 'recon-all -s $(subj) -maskbfs'. Doing this command by hand after the error permits a repeated 'recon-all -make all' command to continue happily. One plausible place to fix this is in bin/recon-all.makefile, at or about line 83-84:

$(BRAIN): $(BRAINMASK) $(NORM) recon-all -s $(subj) -normalization2 recon-all -s $(subj) -maskbfs

i.e. add the step for making the brain masked brain.finalsurfs.mgz file after the -normalization2 step. Would this be correct, and should I do this or something like it?

Sincerely, Greg _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

This is problem was created when FSL 4.0 was made the default. To fix it,

setenv FSLDIR /usr/pubsw/packages/fsl/3.3.2

or

setenv FSLDIR /usr/pubsw/packages/fsl/3.3.7-rh9

then source stable or dev

doug

Pratap Kunwar wrote:

Dear All,

I am a new user of FreeSurfer. I am getting the following error when i run spatialsmooth-sess command.

ERROR: cannot find /usr/local/freesurfer/stable4/fsl/bin/ip ERROR: ipfsl failed

Also, I could not find ip in the bin folder.

Will appreciate for help

sincerely, pratap

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer