[Freesurfer] freesurfer-Darwin-snowleopard-i686-dev.tar.gz is only 167 MB

Hi Freesurfers, Thank you for all the work your team has done on FreeSurfer. Martin Teicher and I are finalizing a manuscript identifying sensitive exposure periods when hippocampal subfields appear to be most vulnerable to the effects of childhood maltreatment using version 5.3 in a sample of

Re: [Freesurfer] A few problems with freesurfer-Darwin-snowleopard-i686-dev-20150507

script, which also incorporates two other changes from > your 'dev' recon-all. The changes are to revert to trilinear > interpolation during the conformed volume creation (matching v5.3) and > to no use our -fix-mtl flag during mris_make_surfaces (which did not > exist in v5.3)

[Freesurfer] quantifyHippocampalSubfields.sh fails in the current version of freesurfer-Darwin-snowleopard-i686-dev.tar.gz

Hi All, I have been using the quantifyHippocampalSubfields.sh from build 20150507 with no problems. However when I try to run the script in the new build (20150610) it fails if I run with the "T1" flag or without. here is the result with T1: *vermisii:RBrain carlanderson$ quantifyHippocampalSub

[Freesurfer] example in mris_label2annot's help

Dear list, I tried runing the example in mris_label2annot's help: mris_label2annot --s bert --h lh --ctab aparc.annot.ctab --a myaparc --l lh.unknown.label --l lh.bankssts.label --l lh.caudalanteriorcingulate.label --nhits nhits.mgh got the following result: ERROR: cannot find or read aparc.anno

Re: [Freesurfer] example in mris_label2annot's help

Oh yes, /Applications/freesurfer/subjects/bert/label/aparc.annot.ctab On Tue, Mar 25, 2014 at 11:35 AM, Douglas N Greve wrote: > does that file exist? > On 03/25/2014 10:04 AM, Carl Anderson wrote: > > Dear list, > > I tried runing the example in mris_

Re: [Freesurfer] example in mris_label2annot's help

No...I will try running it from lables On Tue, Mar 25, 2014 at 6:04 PM, Douglas N Greve wrote: > > does it exist in the same folder that you are running the command from? > > On 03/25/2014 05:15 PM, Carl Anderson wrote: > > Oh yes, > > > > /Applications/

[Freesurfer] Rejoindre mon réseau sur LinkedIn

LinkedIn Carl Anderson souhaite se connecter à vous sur LinkedIn : -- Je vous invite à faire partie de mon réseau professionnel en ligne sur le site LinkedIn. Accepter l'invitation de Carl Anderson http://www.linkedin.

[Freesurfer] Problem with mri_glmfit ill-conditioned matrix

Dear Freesurfer, We have a recurrent problem with an ill-conditioned matrix. Could someone shed some light on our problem. Here is the command line: mri_glmfit --y lh.ELS-CON.thickness.10.mgh --fsgd CAT-SP_June26.FSGF dods --C ELSvsCON_COV-Gen-Age-ICV.mtx --surf fsaverage lh --cortex --glmdi

[Freesurfer] problem with qdec in full install of 5.2 beta

Dear Freesurfer, When trying to start qdec I get the following error: dyld: Library not loaded: /opt/X11/lib/libGLU.1.dylib Referenced from: /Applications/freesurfer/bin/qdec.bin Reason: image not found Trace/BPT trap Any suggestions for a work around? Thanks, Carl -- <<•>>~<>~<<•>>~<>~<

Re: [Freesurfer] "error parsing license file, expected 4 values" with amygdala segmentation

Hi Andrew, Looks like only 3 lines. I'll see if I can locate a back up. Thanks, Carl On Wed, Nov 15, 2017 at 3:06 PM, Hoopes, Andrew wrote: > Hi Carl, > > How many lines of text exist in your license file? > > Andrew > > On Nov 9, 2017, at 8:18 AM, Carl Anderson wro

Re: [Freesurfer] new paper published

Hi Bruce, Would it be possible to get a reprint? I no longer have Harvard Library access. Thanks, Carl On Tue, Dec 5, 2017 at 4:46 PM, Bruce Fischl wrote: > Hi All > > we just published a paper on 3D microscopic imaging of connectivity and > architecture: > > https://www.sciencedirect.com/sc

[Freesurfer] kvlThresholdImage fails MacOSX 10.6.8

Dear Freesurfer, I am using a 2 x 2.66 Ghz 6-Core Intel Xeon with 24Gb RAM and MacOSX 10.6.8 I tried running kvlThresholdImage from /subject/mri/ which resulted in the following error: -- kvlThresholdImage orig.mgz /Applications/freesurfer/subjects/repeats/n10a/mri/orig/002.mgz

[Freesurfer] Stupid FsFastTutorialV5.1/TutorialData question

Dear Free Surfer, At the bottom of http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastTutorialV5.1/TutorialData it is stated: "You will also need to link the FreeSurfer anatomical subjeccts (data in fsfast-tutorial.subjects) into your $SUBJECTS_DI

[Freesurfer] ERROR running mkcontrast - in FsFastTutorialV5.1

Dear Free Surfer, I have gotten to 3. Configure Contrasts in http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastTutorialV5.1/FsFastFirstLevel When I run *mkcontrast-sess -analysis my-workmem.sm05.lh -contrast encode-v-base -a 1* I get the following result and error: vermisii:fsfast-functional carla

Re: [Freesurfer] mac os questions and hypo/hyper intensity question

Hi Lindsay, I have run FS on Lion (10.7.2) on a MacBook Pro with excellent results. Don't know about hypo&hyper. Carl On Wed, Nov 30, 2011 at 4:02 PM, Lindsay Ercole wrote: > Has anyone else had problems installing FS 5.1 on a Mac running OS 10.7.2? > (i.e. Lion) > > Also - are the hypo and hy

[Freesurfer] List of midpoint talairach coordinates for each FreeSurfer cortical region?

Dear FreeSurfers, Anyone out there know of a list of talairach coordinates for FreeSurfer cortical regions (MNI? I suppose)? Thanks! Carl -- <<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>> Carl M. Anderson, Ph.D. (mail stop 204) Assistant Professor of Psychiatry, Harvard M

[Freesurfer] mri_segstats for T2-relaxation time data?

g aseg.mgz \ --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt \ --i T1.mgz \ --sum T1.stats produces a text file 'T1.stats' which has stats on each aseg struct as taken from the vol T1.mgz. n. On Thu, 2010-12-30 at 17:52 -0500, Carl Anderson wrote: > Dear Freesurfer

[Freesurfer] Version 4.2.0 for Tiger on PowerPC Mac?

Hi Would it be possible to somehow download V4.2.0 for Tiger running on a PowerPC Mac? Thanks --- Carl M. Anderson, Ph.D. Assistant Professor of Psychiatry, Harvard Medical School & The Neural Imaging Center, McLean Hospital 115 Mill St. Belmon

[Freesurfer] How to reorient brains collected headfirst prone

Dear Freesufers, How do I preprocess for freesurfer, heads collected headfirst prone instead of the normal headfirst supine? Thanks, Carl --- Carl M. Anderson, Ph.D. Assistant Professor of Psychiatry, Harvard Medical School & The Brain Imaging

[Freesurfer] Am I losing T2* info in MEMPRAGE data by differential scaling?

Dear Freesurfer, I am concerned that I may not be processing the MEMPRAGE images to full take advantage of the T2* info in the multi-echos. I have been separating each echo as 001.mgz, 002.mgz, 003.mgz & 004.mgz when using recon-all. This works well if motion exists in any of the individual echo

Re: [Freesurfer] Am I losing T2* info in MEMPRAGE data by differential scaling?

he echoes. All four echoes >> for each line of k-space are acquired within 20ms of each other. >> >> Carl Anderson wrote: >> >>> Dear Freesurfer, >>> >>> I am concerned that I may not be processing the MEMPRAGE images to >>> full take ad

[Freesurfer] GroupAnaysis Tutorial question: GLM directory error

Dear Freesurfer, My current subjects dir is: /Applications/freesurfer/subjects/buckner_data/tutorial_subjs/group_analysis_tutorial When I run the following (from the tutorial): mri_glmfit-sim --glmdir lh.gender_age.glmdir --sim mc-z 5 4 mc-z.negative --sim-sign neg --overwrite I get the follow