Hi Bruce,
I?ve attached a screen shot of a temporal pole of one of the brains that we have had issues with. Here the issue is that there is a lesion without a very clear boundary for the white matter and freesurfer was unresponsive to simply using white matter edits (placing 255s on the wm.mgz), and so we tried placing control points where we think the white matter boundary should lie. However, we know that control points should not be placed in these dark spots of a lesion.
Thank you,
Allison
Dear FreeSurfer experts,
I have a question regarding the Monte Carlo correction. To create a Monte Carlo correction for my specific sample (4year old kids) the wiki suggests this command: mri_mcsim --o $FREESURFER_HOME/average/mult-comp-cor/yoursubject/lh/cortex --base mc-z --surface yoursubject lh --nreps 10000
I have run this command, however I get an error message that I have no rights to write into the $FREESURFER_HOME directory. I work at an institute where that directory is stored on a server to which many people have access but no writing rights (which is definitely a good thing), so getting the rights is not really an option. I was wondering now whether I could just specify a different directory or whether it absolutely has to be the $FREESURFER_HOME directory? If the latter is the case, would you suggest I install a local copy or do you have any other suggestions?
Thanks in advance! Clara
You can just store it in a different directory, then use the --cache-dir option when running mri_glmfit-sim to specify the new folder, eg, if you use --o /path/to/myspace/yoursubject/lh/cortex, then specify /path/to/myspace
On 03/15/2016 12:36 PM, Clara Kühn wrote:
Dear FreeSurfer experts,
I have a question regarding the Monte Carlo correction. To create a Monte Carlo correction for my specific sample (4year old kids) the wiki suggests this command: mri_mcsim --o $FREESURFER_HOME/average/mult-comp-cor/yoursubject/lh/cortex --base mc-z --surface yoursubject lh --nreps 10000
I have run this command, however I get an error message that I have no rights to write into the $FREESURFER_HOME directory. I work at an institute where that directory is stored on a server to which many people have access but no writing rights (which is definitely a good thing), so getting the rights is not really an option. I was wondering now whether I could just specify a different directory or whether it absolutely has to be the $FREESURFER_HOME directory? If the latter is the case, would you suggest I install a local copy or do you have any other suggestions?
Thanks in advance! Clara
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Thanks a lot! I will do that then :)
Cheers, Clara
----- Ursprüngliche Mail ----- Von: "Douglas N Greve" greve@nmr.mgh.harvard.edu An: freesurfer@nmr.mgh.harvard.edu Gesendet: Dienstag, 15. März 2016 17:40:08 Betreff: Re: [Freesurfer] adapt Monte Carlo correction for specific sample
You can just store it in a different directory, then use the --cache-dir option when running mri_glmfit-sim to specify the new folder, eg, if you use --o /path/to/myspace/yoursubject/lh/cortex, then specify /path/to/myspace
On 03/15/2016 12:36 PM, Clara Kühn wrote:
Dear FreeSurfer experts,
I have a question regarding the Monte Carlo correction. To create a Monte Carlo correction for my specific sample (4year old kids) the wiki suggests this command: mri_mcsim --o $FREESURFER_HOME/average/mult-comp-cor/yoursubject/lh/cortex --base mc-z --surface yoursubject lh --nreps 10000
I have run this command, however I get an error message that I have no rights to write into the $FREESURFER_HOME directory. I work at an institute where that directory is stored on a server to which many people have access but no writing rights (which is definitely a good thing), so getting the rights is not really an option. I was wondering now whether I could just specify a different directory or whether it absolutely has to be the $FREESURFER_HOME directory? If the latter is the case, would you suggest I install a local copy or do you have any other suggestions?
Thanks in advance! Clara
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Maybe you can draw the wm in? I wouldn't put control points there
On Mar 15, 2016, at 9:13 AM, Allison Rainford allison.rainford@northwestern.edu wrote:
Hi Bruce,
I?ve attached a screen shot of a temporal pole of one of the brains that we have had issues with. Here the issue is that there is a lesion without a very clear boundary for the white matter and freesurfer was unresponsive to simply using white matter edits (placing 255s on the wm.mgz), and so we tried placing control points where we think the white matter boundary should lie. However, we know that control points should not be placed in these dark spots of a lesion.
Thank you,
Allison
<Screen Shot 2016-03-14 at 4.56.13 PM.png> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Bruce Fischl -
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Douglas N Greve