Re: [Freesurfer] Group analysis over different studies?

Just run isxconcat-sess for each study, then mri_concat study1/gamma.mgh study2/gamma.mgh --o study1-and-study2-gamma.mgh then run mri_glmfit on the above output doug On 6/16/14 11:54 PM, Terri Scott wrote: Hi all, I want to do a group analysis using subjects that were run in different st

Re: [Freesurfer] Using QDEC for 3 groups x 2 time-points

It only needs to be accounted for when you compare across all 3 groups, in which case you'd have to use mri_glmfit doug On 6/17/14 12:07 AM, Tudor Popescu wrote: Hi Doug, Thanks... Presumably I'd just leave each possible pair of groups at a time in the qdec table, and delete rows correspon

Re: [Freesurfer] subcortical segment NIFTI files

On 6/17/14 4:09 AM, Yang, Daniel wrote: Hi Doug, I see. It works well. Just curious, when should we use reg.2mm.mni152.dat then? It is used mostly in FSFAST Also curious, what is $FREESURFER_HOME/average/mni152.register.dat created? I performed a registration between the MNI305 (ie, fsaver

Re: [Freesurfer] Version 5.3 recon-all run time

When in doubt, check the tissue and surface segmentations (https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/OutputData_freeview) but ultimately celebrations seem to be in order... __ Peter Goodin, BSc (Hons), Ph.D Candidate. Brain and Psychological Sciences Research

[Freesurfer] Version 5.3 recon-all run time

Hi FSers, I have an Ubuntu machine (14.04 LTS) with a quad-core i7 4770k/32gb RAM and recon-all is taking me approximately 6 hours per subject without using openmp (haven't tried this yet). According to the terminal, it finishes without errors. I've read (e.g., https://surfer.nmr.mgh.harvard.edu/f

Re: [Freesurfer] subcortical segment NIFTI files

Hi Doug, Could you show us the full command of performing such a registration? Very curious! Thanks. Best, Daniel From: Douglas Greve mailto:gr...@nmr.mgh.harvard.edu>> Reply-To: Freesurfer support list mailto:freesurfer@nmr.mgh.harvard.edu>> Date: Tuesday, June 17, 2014 at 4:30 AM To: "frees

Re: [Freesurfer] subcortical segment NIFTI files

I think I just ran something like bbregister --mov MNI152_T1_2mm.nii.gz --s fsaverage --t1 --reg reg.dat --init-fsl Maybe I tweeked it manually On 6/17/14 1:10 PM, Yang, Daniel wrote: Hi Doug, Could you show us the full command of performing such a registration? Very curious! Thanks. B

Re: [Freesurfer] Tracula preprocessing error ( set dob0 = 1 )

Hi Anastasia, Yes, launching the same command line from terminal produced the same error, but at the same time we realized we were using the wrong magnetic/phase dicoms.which weren't magnetic/phase images at all.Could that be the cause of the failure? I would answer the question myself but r

Re: [Freesurfer] subcortical segment NIFTI files

Hi Doug, Thanks! I ran this: bbregister --mov $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz --s fsaverage --t1 --reg 1mmreg.dat --init-fsl And obtained the following: fsaverage 1.00 1.00 0.15 9.999634623527527e-01 -4.681387450546026e-03 7.184753660112619e-03 1.294338703155518e+

Re: [Freesurfer] Tracula preprocessing error ( set dob0 = 1 )

Hi Elia - This could very well be the case. Does the epidewarp.fsl command give you any specific error message, or does it just not create an output? a.y On Tue, 17 Jun 2014, Elia S. wrote: Hi Anastasia, Yes, launching the same command line from terminal produced the same error, but at the

Re: [Freesurfer] Tracula preprocessing error ( set dob0 = 1 )

Hi Anastasia, The epidewarp.fsl gives me the following output: FSLVersion 5.0.6FSLVerMaj 5FSL Version is 5.0.6, must be 3.X or 4.X Either from script or command line. Best,Elia. Date: Tue, 17 Jun 2014 09:17:58 -0400 From: ayend...@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Subject: Re

Re: [Freesurfer] Tracula preprocessing error ( set dob0 = 1 )

Check the email archives for a recent message about epidewarp.fsl from Doug, there is a newer version that works with FSL 5. On Tue, 17 Jun 2014, Elia S. wrote: Hi Anastasia, The epidewarp.fsl gives me the following output: FSLVersion 5.0.6 FSLVerMaj 5 FSL Version is 5.0.6, must be 3.X or

Re: [Freesurfer] Tracula preprocessing error ( set dob0 = 1 )

Hi Anastasia, Found it, I'll replace it right away, thanks :) Best,Elia. Date: Tue, 17 Jun 2014 09:29:14 -0400 From: ayend...@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Tracula preprocessing error ( set dob0 = 1 ) Check the email archives for a recent mess

Re: [Freesurfer] CSF volume

Hi Bruce, Thanks for your reply! I had a couple follow up questions: 1) In order to calculate the total ventricular CSF, should I add the CSF volume reported in the aseg.stats file to the other ventricular volumes or no? 2) Would there be a way to segment the sulcal CSF based on the T2 image? T

Re: [Freesurfer] Number of Slices

Thanks Bruce. Also for running recon-all on the T1 - in terms of motion correction, is it better to run it with one nifti file converted from all the dicoms (therefore 1 input), or all of the dicom files (if this is even possible)? Caroline On Mon, Jun 16, 2014 at 2:58 PM, Bruce Fischl wrote:

[Freesurfer] Retinotopic mapping using selxavg3-sess

Hello, I'm using freesurfer to do retinotopic mapping. I've completed the recon-all, mkanalysis-sess, mri-convert and preproc-sess steps. Now when I run the selxavg3-sess (my subject name is 3): selxavg3-sess -a Retinotopy.3.lh -s 3 I got the following message: "ERROR: /usr/local/fre

[Freesurfer] fsfast preproc question

The volume produced from the -mni305 option in preproc-sess, does not look like a brain (it seems to be mostly cerebellum. I have attached an image). Is this the expected behavior? I have included the relevant path and information below: source /cluster/neuromind/dwakeman/wmh/software/nmr-stable53

Re: [Freesurfer] problem of Label file

Hi Wang no, it doesn't seem correct. What was the overlay when you created the label? cheers Bruce On Tue, 17 Jun 2014, 王康程 wrote: Hi all, I create a label file according to my result using QDEC, does it correct? why some number is so large? #!ascii label , from subject vox2ras=TkReg 2

Re: [Freesurfer] Version 5.3 recon-all run time

yes, the 20-24 hour numbers are several years old at this point, and we have made some improvements to speed so 6 hours is not unheard of. That said, definitely visually inspect the results! I'll leave the hyperthreading question for Zeke or Nick cheers Bruce On Tue, 17 Jun 2014, Peter Goodin

[Freesurfer] Improving translation of Choi striatal ROIs to original domain

Hi Freesurfers, My processing stream involves moving the parcellated functional networks of Yeo and Choi to original subject domain to do connectivity analyses. While my process works very well for the Yeo networks I'm rather unsatisfied by the results of the Choi translations. I'm hoping someone

Re: [Freesurfer] CSF volume

1. No, just add up all the ventricle measures. 2. I think FSL might do this, but you would probably have to mask out the ventricles as I doubt they label sulcal csf separately On Tue, 17 Jun 2014, pfot...@nmr.mgh.harvard.edu wrote: > Hi Bruce, > > Thanks for your reply! I had a couple follow u

Re: [Freesurfer] Number of Slices

give it one slice in every dicom series and it will figure out the rest. If you specify more than one series (with more than one -i it will do motion correction and averaging. cheers Bruce On Tue, 17 Jun 2014, Caroline Lewis wrote: Thanks Bruce. Also for running recon-all on the T1 - in ter

Re: [Freesurfer] fsfast preproc question

Yes, it is masked to subcortical gray matter doug On 6/17/14 4:18 PM, dgw wrote: The volume produced from the -mni305 option in preproc-sess, does not look like a brain (it seems to be mostly cerebellum. I have attached an image). Is this the expected behavior? I have included the relevant pa

[Freesurfer] Brining Freesurfer colomaps and/or lookup table to MRIcron

Dear Freesurfers, Is there a way to bring the colormaps of Freesurfer to MRIcron. Right now when I bring parcellations in MRIcron there is no good way to distinguish parcels, because the parcels are numerated 1000+ for left hemisphere, 2000+ for right, 3000+ for white matter left, etc. This makes

Re: [Freesurfer] Retinotopic mapping using selxavg3-sess

It looks for it in the current folder. You must run this from the same folder you ran mkanalysis-sess from (which should be your project folder) On 6/17/14 4:13 PM, Alan Lee wrote: Hello, I'm using freesurfer to do retinotopic mapping. I've completed the recon-all, mkanalysis-sess, mri-co

[Freesurfer] mni/bin/nu_correct: Exec format error. Binary file not executable.

I have cruised the mailing list for 5.3 specific causes. Some runs work and some hit this error.recon-all -autorecon1 -skullstrip -gcut -subjid 1217_1 We are crunching a set of over 300 and I have checked the obvious. This is what I downloaded: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0

Re: [Freesurfer] subcortical segment NIFTI files

Thanks! Does bbregister use orig.mgz in --s? If yes, I guess I should use MNI152_T1_1mm.nii.gz instead, since it has skull, like $FREESURFER_HOME/subjects/fsaverage/mri/orig.mgz. Daniel From: Douglas Greve mailto:gr...@nmr.mgh.harvard.edu>> Reply-To: Freesurfer support list mailto:freesurfer

Re: [Freesurfer] Group analysis over different studies?

Hi Doug, Is gamma.mgh the same as ces.nii.gz? I'm working with data processed with an older version of Freesurfer, not exactly sure which. I have a related question also; the masks and meanfunc images don't seem to be lining up that well after running isxconcat-sess. Would is be possible for me to

Re: [Freesurfer] Version 5.3 recon-all run time

Linden, Its my understanding that that with hyperthreading enabled, you can run a subject for each processor the computer "thinks" it has. For instance, on CentOS (Im not sure the equivalent command on Ubuntu) if I 'cat /proc/cpuinfo' I see 4 processors listed. In this case I would be able to

[Freesurfer] FreeSurfur Installation problems

Hello, I am having issue with running Tkmedit, tksurfer, qdec, and recon-all. Based on the error messages I am receiving, it appears that the program think I have permission issues. I have checked these and that does not appear to be the case. Here are the errors I am getting. Please let me kno

[Freesurfer] free surfer

I have downloaded the following file freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz and have extracted the contained files, and I was wondering where the binary file is so that I can open the freesurfer with? thanks -S __

Re: [Freesurfer] free surfer

Hi, You can see here what to do: https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall no 4., 5 and 6 especailly. Cheers, M 2014-06-18 0:45 GMT+02:00 Sam Raby : > I have downloaded the following file > > freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz > > and have extracted the

Re: [Freesurfer] Version 5.3 recon-all run time

Hi Peter, Bruce, and Zeke, Thank you all for the various input. According to the tutorial Peter posted, the handful of subjects I've done look good. I ran another subject with -openmp 4 flag and it shaved the processing down to <4 hours, so that is a very nice saving! The System Monitor app in Ubu

Re: [Freesurfer] Version 5.3 recon-all run time

Linden, The fastest runtime that I have seen is just under 3.5 hours using a new and very fast system such as yours, using the -openmp 8 flag. Processing four participants in separate tcsh sessions is the recommended way of 'parallel' processing. There are flags in recon-all to allow splitting t

[Freesurfer] question about recon-all autorecon2 "Automatic Topology Fixer"

Hi! I am a relative beginner with freesurfer and was going through the steps listed on freesurfer wiki about detailed description of each steps autorecon2 covers. During "Automatic Topology Fixer (-fix)", the description stated that "user should check the orig surface in the volume to make sure

Re: [Freesurfer] question about recon-all autorecon2 "Automatic Topology Fixer"

Hi Cheng why can't you visualize them? You should be able to load them on the command line in freeview via: freeview -f surf/lh.orig surf/lh.orig.nofix or from the GUI. cheers Bruce On Tue, 17 Jun 2014, Cheng Peng wrote: Hi! I am a relative beginner with freesurfer and was going through