[Freesurfer] fdr correction problem

2018-12-10 Thread 1013364183
External Email - Use Caution Dear Bruce?? I have fdr correction for sig.mgh obtained by mri_glmfit, but the corrected graphs are all 0. Why is this, the instructions and the running results are as follows: mri_fdr --fdr .05 --i lh2.gender_age.glmdir/group2/sig.mgh lh2.gender

[Freesurfer] fdr correction problem

2018-12-10 Thread 1013364183
External Email - Use Caution Dear Bruce?? I have fdr correction for sig.mgh obtained by mri_glmfit, but the corrected graphs are all 0. Why is this, the instructions and the running results are as follows: mri_fdr --fdr .05 --i lh2.gender_age.glmdir/group2/sig.mgh lh2.gender

[Freesurfer] LGI error

2018-12-10 Thread Lorenzo Ferri
External Email - Use Caution Dear expert I am trying to calculate LGI for a subject. Now with some of your suggestions it runs, but after one hour and half it gives me this errors remeasuring lGI value for vertex iV = 29501. It may take a few minutes. WARNING -- Problem for vert

Re: [Freesurfer] Extracting ROI from atlases

2018-12-10 Thread Song, Da-Yea
External Email - Use Caution Hi Bruce, I've taken a look at the mri_annotation2label command and it seems like it requires a specific subject to run this command. We were looking to pull out the ROI from the Desikan atlas (rather than from a particular participant). Is there a

Re: [Freesurfer] Extracting ROI from atlases

2018-12-10 Thread Song, Da-Yea
External Email - Use Caution Hi Bruce, Will the mri_annotation2label work on /usr/local/Freesurfer/subjects/fsaverage/label/lh.aparc.annot? Thanks, Da-Yea -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu]

Re: [Freesurfer] Extracting ROI from atlases

2018-12-10 Thread Bruce Fischl
yes, it should On Mon, 10 Dec 2018, Song, Da-Yea wrote: External Email - Use Caution Hi Bruce, Will the mri_annotation2label work on /usr/local/Freesurfer/subjects/fsaverage/label/lh.aparc.annot? Thanks, Da-Yea -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu

Re: [Freesurfer] Extracting ROI from atlases

2018-12-10 Thread Bruce Fischl
yes, do it on fsaaverage and it will more-or-less be in the common coordinate space. cheers Bruce On Mon, 10 Dec 2018, Song, Da-Yea wrote: External Email - Use Caution Hi Bruce, I've taken a look at the mri_annotation2label command and it seems like it requires a specific subject to

Re: [Freesurfer] Error in running make_average_subject

2018-12-10 Thread Emanuel Alvaredo
External Email - Use Caution Thanks Bruce. The following is the command. make_average_subject --out avgsubjectPRUEBAESTASIEmac --subjects subject1 subject2 subject3 And I made a mistake in may last mail. I use the word path instead of patch I have found this page with a *pat

[Freesurfer] Increasing the Number of a non-FreeSurfer Parcellation

2018-12-10 Thread Maedeh Khalilian
External Email - Use Caution Dear experts, I have a question, if I have a parcellation which is not the output of FreeSurfer, can i increase the number of its parcels in FreeSurfer? Maybe if I can change my file into an annotation file is it possible? I would be grateful if u

Re: [Freesurfer] Increasing the Number of a non-FreeSurfer Parcellation

2018-12-10 Thread Bruce Fischl
Hi Maedeh I'm not sure I understand. Are you trying to import an existing parcellation that has more parcels than the ones we use? Or something else? If the former, is the parcellation already on the surface? If so, you can always use our matlab tools to write it into an annotation file that we

Re: [Freesurfer] glm analysis

2018-12-10 Thread Barletta, Valeria
Dear Freesurfers, I am trying to run a GLM analysis with 3 groups (1)long disease duration MS, 2)short disease duration MS, 3)healthy controls) and 1 variable (age). According to the formula provided on freewiki: N classes (N of variables + 1), is this contrast matrix correct? 1 -1 0 0 0 0

[Freesurfer] Classification of amygdala subregions using Freesurfers new Algorithm

2018-12-10 Thread Sally Grace
External Email - Use Caution Dear Eugenio and experts, I have run the segmentation of the hippocampus subfields and nuclei of the amygdala using the latest algorithm implemented in the development version of Freesurfer. We have a priori hypotheses regarding the basolateral amyg

Re: [Freesurfer] [EXTERNAL] Re: mri_surf2vol: has many more faces than vertices

2018-12-10 Thread Winkelbeiner, Stephanie A
External Email - Use Caution Hi Douglas, I was wondering if I can use an annot file in surf2vol to project those parcels into the FA image space? Or would label2vol be more appropriate? Bruce was so kind to give me his advice already and we discussed my challenges a bit (see bel

[Freesurfer] Fwd: fcseedcor output

2018-12-10 Thread Sara Jafakesh
External Email - Use Caution -Original Message- From: "Sara Jafakesh" To: freesurfer@nmr.mgh.harvard.edu Cc: dgr...@mgh.harvard.edu Date: Sat, 08 Dec 2018 22:25:20 +0330 Subject: Fwd: fcseedcor output -Original Message- From: "Sara Jafakesh" To: "Greve, Dougla

Re: [Freesurfer] Fwd: fcseedcor output

2018-12-10 Thread Greve, Douglas N.,Ph.D.
Is matlab in your path? What happens when you run which matlab On 12/10/2018 06:12 PM, Sara Jafakesh wrote: > > External Email - Use Caution > > > -Original Message- > From: "Sara Jafakesh" > To: freesurfer@nmr.mgh.harvard.edu > Cc: dgr...@mgh.harvard.edu > Da