[Freesurfer] Postdoctoral position available, Paderborn (Germany)

The Institute of Sports Medicine at the University of Paderborn invites applications for a full-time Postdoctoral Position to conduct, process and analyze EEG and other neuroimaging data in the context of sports and exercise. The primary responsibility of this position includes developing nov

Re: [Freesurfer] Cortical reconstruction

Dear Bruce, Many thanks for your answer. All the best, Mohamed On 11/01/16 14:40, Bruce Fischl wrote: > Hi Mohamed > > you can use mri_synthesize to create a flash image with good T1 contrast > from quantitative maps and run it through recon-all. > > cheers > Bruce > On Mon, 11 Jan 2016, > Moha

[Freesurfer] QDEC. Error in Analyze: command failed: mri_glmfit

Hi there experts, I'm runing qdec to analyze my subject data. I am able to import the qdec.table.dat, but the problem comes in the Design step. I select 'Volume-based' measure, 'Diagnosis' as my discrete independent variable and 'LeftAmygdala' as the continuous variable. I don't select any nuis

[Freesurfer] Visualizing GLM analysis error

Hello all, I am trying to visualize the results of my GLM analysis. Unfortunately, I keep on running into errors. I run the command: freeview -f $SUBJECTS_DIR/fsaverage/surf/lh.inflated:annot=aparc.annot:annot_outline=1overlay=lh.Cog_Trial1.glmdir/lh-Avg-thickness-Cog_Trial1/sig.mgh:

Re: [Freesurfer] Visualizing GLM analysis error

Hi Peter you need a colon to separate each of the modifiers you are using, not a space. So freeview -f lh.inflated:annot=aparc.annot:outline=1:overlay= cheers Bruce On Thu, 14 Jan 2016, Myers, Peter wrote: Hello all, I am trying to visualize the results of my GLM analysis. Unfortunate

Re: [Freesurfer] Visualizing GLM analysis error

also, I think that the annot_outline is a version 6 feature. On 1/14/16 1:01 PM, Bruce Fischl wrote: Hi Peter you need a colon to separate each of the modifiers you are using, not a space. So freeview -f lh.inflated:annot=aparc.annot:outline=1:overlay= cheers Bruce On Thu, 14 Jan 2016,

[Freesurfer] Visualizing GLM analysis error

Thanks for these comments/suggestions. Still having troubles unfortunately. I ran the command:  freeview -f $SUBJECTS_DIR/fsaverage/surf/lh.inflated:annot=aparc.annot:overlay=lh.Cog_Trial1.glmdir/lh-Avg-thickness-Cog_Trial1/sig.mgh:overlay_threshold=4,5 -viewport 3d I don't think there ar

Re: [Freesurfer] Visualizing GLM analysis error

can you run mri_info on that file? Is it in fact a surface overlay? On Thu, 14 Jan 2016, Myers, Peter wrote: Thanks for these comments/suggestions. Still having troubles unfortunately. I ran the command:  freeview -f$SUBJECTS_DIR/fsaverage/surf/lh.inflated:annot=aparc.annot:overlay=lh.Cog

[Freesurfer] FW: FW: problem with hard coded directory (/scratch)

Hi FS's experts, I sent out a couple of emails to seek for help on an error from running recon-all using freesurfer 6.0 beta. Could anyone help with the question? Thank you! - Fengji From: Fengji Geng Sent: Thursday, January 07, 2016 8:15 AM To: freesurfer@

Re: [Freesurfer] Visualizing GLM analysis error

It's working now! Thank you everyone for your help. Some settings in the GUI seemed off for some reason. From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Bruce Fischl Sent: Thursday, January 14, 2016 12:39 PM To: Freesurfer support list Subject:

Re: [Freesurfer] Visualizing GLM analysis error

glad to hear it On Thu, 14 Jan 2016, Myers, Peter wrote: > It's working now! > Thank you everyone for your help. > Some settings in the GUI seemed off for some reason. > > From: freesurfer-boun...@nmr.mgh.harvard.edu > on behalf of Bruce Fischl > > Sent

Re: [Freesurfer] FW: FW: problem with hard coded directory (/scratch)

Hi Fengji, Sorry for the late reply; I was on vacation and totally missed your question. The hippocampal subfield module uses /scratch to create temporary files if available. If not, it creates a directory under the tmp directory inside the subject directory. It was coded this way because in ou

Re: [Freesurfer] FW: FW: problem with hard coded directory (/scratch)

Hi Fengji, you have sent several emails. I keep asking you to give us a specific binary that has the problem, but you seem to ignore my request, wait a couple of weeks, then post the question back to the list. I'm happy to take look, but please send me something more specific! thanks doug On

[Freesurfer] Register surface ROI across hemisphere and into volume

Hi freesurfer list. I have a surface label for a region-of-interest in the right hemisphere, which I generated from a cortical thickness analysis. I am now doing an analysis on the white matter below this roi, by moving the label into volume space with mri_label2vol, and sampling below the surface

Re: [Freesurfer] Interpreting white matter regressor dat file

Hi Doug, These are the first few lines of the wm.dat.pca-stats.dat file: 1 143481216.00 143481216.00 4.064.06 2 77359288.00 220840504.00 2.196.25 3 42542944.00 263383448.00 1.207.46 4 26329902.00 289713350.00 0.758.20 5 21830372.00 31154372

[Freesurfer] (no subject)

-- Jasmin Alves Predoctoral Student Medical Biology Graduate Program University of Southern California jal...@usc.edu ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The informatio

[Freesurfer] (no subject)

Hello, I recently downloaded freesurfer on my mac with a Yosemite operating system. The application itself appears to work, however I am not able to use the command line to do any of the testing free surfer commands, as I keep getting a access denied. I have attached a screenshot. Your help would

Re: [Freesurfer] QDEC. Error in Analyze: command failed: mri_glmfit

how many levels does factor 1 have? How did you make the factor file? On 01/14/2016 05:30 AM, BAUTISTA-PERPINYA Maximilià wrote: > Hi there experts, > > I'm runing qdec to analyze my subject data. I am able to import the > qdec.table.dat, but the problem comes in the Design step. I select > 'Vol

Re: [Freesurfer] (no subject)

Hi Jasmin, do you have permission to execute FS commands? What is the result of ls -l $FREESURFER_HOME/bin/tksurfer On 01/14/2016 04:16 PM, Jasmin Alves wrote: > Hello, > > I recently downloaded freesurfer on my mac with a Yosemite operating > system. The application itself appears to work, ho

Re: [Freesurfer] (no subject)

Hi Dr. Greve, I am still receiving the same message that I am denied access to freeview. Is there anything I can do? Thanks, Jasmin On Thu, Jan 14, 2016 at 1:22 PM, Douglas N Greve wrote: > Hi Jasmin, do you have permission to execute FS commands? What is the > result of > ls -l $FREESURFER_HO

Re: [Freesurfer] (no subject)

Here is the output to the ls command On Thu, Jan 14, 2016 at 1:55 PM, Jasmin Alves wrote: > Hi Dr. Greve, > > I am still receiving the same message that I am denied access to freeview. > Is there anything I can do? > > Thanks, > Jasmin > > On Thu, Jan 14, 2016 at 1:22 PM, Douglas N Greve < > gr.

Re: [Freesurfer] (no subject)

Jasmin, can you just cut and paste it into the email? On 01/14/2016 04:59 PM, Jasmin Alves wrote: > Here is the output to the ls command > > On Thu, Jan 14, 2016 at 1:55 PM, Jasmin Alves > wrote: > > Hi Dr. Greve, > > I am still receiving the same message that I am

Re: [Freesurfer] (no subject)

Jasmins-MacBook-Pro:freesurfer jasminalves$ ls -l $FREESURFER_HOME/bin/tksurfer -rwxr-xr-x 1 root wheel 103 May 14 2013 /Applications/freesurfer/bin/tksurfer Jasmins-MacBook-Pro:freesurfer jasminalves$ $> freeview -v $SUBJECTS_DIR/bert/mri/brainmask.mgz -v $SUBJECTS_DIR/bert/mri/aseg.mgz:col

Re: [Freesurfer] (no subject)

Jasmin, Did you follow the instructions from the wiki: https://surfer.nmr.mgh.harvard.edu/fswiki/QuickInstall which links to this mac specific page. https://surfer.nmr.mgh.harvard.edu/fswiki/MacOsInstall ? hth d On Thu, Jan 14, 2016 at 5:10 PM, Jasmin Alves wrote: > Jasmins-MacBook-Pro:freesu

Re: [Freesurfer] (no subject)

Yes I did. I was on the last step, the testing freesurfer when I discovered the commands do not work On Thu, Jan 14, 2016 at 2:14 PM, dgw wrote: > Jasmin, > > Did you follow the instructions from the wiki: > > https://surfer.nmr.mgh.harvard.edu/fswiki/QuickInstall > which links to this mac speci