[Freesurfer] Hippocampal subfield tool for 6.0.0 data

External Email - Use Caution Hello, Would you be able to point me to the right version of the hippocampal subfield tool as described here: https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldsAndNucleiOfAmygdala? The data have been processed in 6.0.0, but the stable

Re: [Freesurfer] Comparison between T1 only recon-all and T1 + FLAIR recon-all

with the FLAIRpial command? Any input would be greatly appreciated. Thanks! From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of O'Shea,Andrew <aos...@phhp.ufl.edu> Sent: Thursday, April 26,

[Freesurfer] Comparison between T1 only recon-all and T1 + FLAIR recon-all

External Email - Use Caution Hello, In the past we have only used the T1 image as input for recon-all. However, we are now also acquiring a FLAIR image and were thinking of using both for new studies. Does anyone have any data on the differences/advantages of using FLAIR

[Freesurfer] Hippocampal Subfields 6.0 with 5.3 recons

Hello all, I was wondering if anyone with knowledge of the new hippocampal subfield segmentation that is going to be released with version 6.0 could answer a quick question. We have previously processed subjects in v5.3 and would like to use the new hippocampal seg algorithm. How "standalone"

Re: [Freesurfer] qdec analysis with ICV

Try mean centering your ICV values (I.e. Subtract the mean value from each individual value). This has worked for me to bypass this error. -Andrew From: > on behalf of "Hirsch, Gabriella"

Re: [Freesurfer] qdec analysis with ICV

ull ICV values. Even with David’s suggestion of reducing the number of digits (effectively making the numbers smaller), it still doesn’t work… Gabriella From: freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> [mailto:freesurfer-boun...@nmr.mgh.harvard.e

[Freesurfer] Hippocampal Subfields 6.0 with 5.3 recons

Hello all, I was wondering if anyone with knowledge of the new hippocampal subfield segmentation that is going to be released with version 6.0 could answer a quick question. We have previously processed subjects in v5.3 and would like to use the new hippocampal seg algorithm. How "standalone"

Re: [Freesurfer] mris_anatomical_stats giving segmentation faults for certain subjects

/dotsonFSprocessed//EX03/surf/rh.white and/or view it in freeview to make sure it isn't corrupted? On Wed, 15 Jul 2015, O'Shea,Andrew wrote: Hello all, I am having an issue where the mris anatomical stats command is failing and only printing ʽsegmentation faultʼ instead of the expected volume, area

[Freesurfer] mris_anatomical_stats giving segmentation faults for certain subjects

Hello all, I am having an issue where the mris anatomical stats command is failing and only printing 'segmentation fault' instead of the expected volume, area, thickness, etc. This is happening for ~20% of the subjects, but seems to work fine for the remaining 80%. All labels were created and

Re: [Freesurfer] Cannot launch tkmedit in Ubuntu RE: Freesurfer Digest, Vol 137, Issue 10

Topics: 1. saving clusters in qdec (O'Shea,Andrew) 2. Re: couple TRACULA questions (Harms, Michael) 3. Repost: What algorithm does mri_label2label use? (Caspar M. Schwiedrzik) 4. Re: Repost: What algorithm does mri_label2label use? (Douglas N Greve) 5. Re: convert FS volume

Re: [Freesurfer] Approximately how many brains do I need to manually edit?

I'm by no means an expert, but I've found that best practice dictates looking at every subject slice by slice. This sounds daunting but I've found you can look through a subject in 10-15 minutes. I don't think you will get a clear answer because the quality of acquisition can vary widely

[Freesurfer] saving clusters in qdec

Hello, Is it possible to save a mask of significant clusters past a certain threshold, say 3.0, directly from the qdec interface? I want to save a few clusters, and then map them back to individual subject space. I see I can do this if I manually trace the cluster and save the ROI, but this not

[Freesurfer] Open MP parallel processing scaling factor?

Hello all, Traditionally I have only processed FS data using a single core per person, but processing many people at once. Now we have caught up with the backlog of scans, we have a continuos trickle of scans coming in 1 by 1. I was wondering if anyone has tested how the speed-up of open-mp

[Freesurfer] Permutation testing in freesurfer

Hello all, Does anyone know of a toolbox/script that would automate permutation testing in freesurfer? For example running x number of random permutations of a covariate and recording max sig levels similar to what the software SnPM does for SPM analyses? Thanks. -Andrew

[Freesurfer] qcache number of vertices error [fixed]

Hello all, I was able to fix my error (see below) by re-running recon-all $SUB –autorecon2 –autorecon3 –qcache . However I am unsure why –make all was not incorporating edits correctly? Is it inappropriate to use –make all after manual edits? If so, should I just use –autorecon2 –autorecon3 as

[Freesurfer] qcache number of vertices error

Hello, I am running into an error when using qcache. Subjects that have had manual edits are exited with errors, while subjects that have not had edits run fine. All subjects have had –make all ran after edits and finished without errors. I have read about this problem and tried some of the

Re: [Freesurfer] When/What to edit?

and not found any effect or rater (all unpublished). Sorry, as I said, I'm not sure how useful any of this is cheers Bruce On Fri, 2 May 2014, O'Shea,Andrew wrote: Hello FS experts, I have had a continuing curiosity regarding when/what to edit in FS cortical reconstructions. The wiki does a good

[Freesurfer] When/What to edit?

Hello FS experts, I have had a continuing curiosity regarding when/what to edit in FS cortical reconstructions. The wiki does a good job at showing how to deal with large scale problems, (i.e. invalid tal transformation, white matter not being recognized, large portions of the skull included in

[Freesurfer] Extracting individuals data at a vertex

Hello FS experts, In QDEC when I click on a vertex a scatter plot is generated with each individuals data for that vertex. Is there a simple way to extract that data (for each subject) into spreadsheet form for a specific vertex? -Andrew ___ Freesurfer

[Freesurfer] Thalamic subdivisions

Hello FS-Experts, I was wondering if there has been any work done to subdivide the thalamus segmentation (aseg volume) into smaller sub-sections, similar to what has been done with the hippocampus (using -hippo-subfields)? I am measuring longitudinal changes in the volume of the thalamus from

Re: [Freesurfer] Problem with FS-FAST, mkcontrast

path? doug On 07/01/2013 08:55 AM, O'Shea,Andrew wrote: Hello, I am trying to work through the FS-FAST tutorial on my data. I am using OSX 10.6.8 with Freesurfer v. 5.1 When I get to the make contrast command which I run ' mkcontrast-sess -analysis test -contrast pain-v-rest -a 1 -c 0 ' I get

[Freesurfer] Problem with FS-FAST, mkcontrast

Hello, I am trying to work through the FS-FAST tutorial on my data. I am using OSX 10.6.8 with Freesurfer v. 5.1 When I get to the make contrast command which I run ' mkcontrast-sess -analysis test -contrast pain-v-rest -a 1 -c 0 ' I get the following output error: phhp-jcraggs-mb:Project

Re: [Freesurfer] Problem with FS-FAST, mkcontrast (Douglas N Greve)

and in your path? doug On 07/01/2013 08:55 AM, O'Shea,Andrew wrote: Hello, I am trying to work through the FS-FAST tutorial on my data. I am using OSX 10.6.8 with Freesurfer v. 5.1 When I get to the make contrast command which I run ' mkcontrast-sess -analysis test -contrast pain-v-rest -a 1 -c 0

[Freesurfer] longitudinal sulci depth change

Hello, I was wondering if I could get some clarification regarding the longitudinal measure of rate of change in sulci depth. In our study we have a patient population that participated in an intervention and a similar group of wait list controls. We have scans for pre and post intervention

Re: [Freesurfer] long_mris_slopes / mris_calc problem

I was able to solve my problem in my earlier email included below. I downloaded a new verison of mris_calc made it executable with chmod +x FILE and then replaced it in the bin folder. I included this response in case anyone else runs into the same problem and does a search.

[Freesurfer] long_mris_slopes / mris_calc problem

Hello Freesurfer experts, I am working on a study that wants to compare pre/post cortical thickness on an intervention group and a control group. I am using FS 5.1 on a Mac. I have processed all the recons through the longitudinal stream as described in the wiki/tutorial. However when I go to

[Freesurfer] motion correction

Hello, Our data set has two T1 weighted scans for some subjects but only one for others. Would you recommend running all subjects with no motion correction (1 scan input)? Also can files be mixed in the analysis that have had motion correction with those who have not? Thanks! -Andrew