[Freesurfer] Freesurfer autorecon2 problem

Dear Freesurfers, I am now trying to do recon-all -autorecon1 and recon-all autorecon2 and then do the quality control. When I try " recon-all -autorecon1 -subjid ADNI_002_S_0559_MR_MPRAGE_br_raw_20080821223915203_1_S55646_I116582 -notal-check " It works. However, next when I do " recon-all -

[Freesurfer] Research Position

Hi Freesurfers, I wanted to bring to the attention of recent graduates a research assistant position in my lab. Briefly, the position entails the application and transfer of your proficiency with FreeSurfer in the acquisition and analysis of fMRI data collected from healthy adults. More detail

Re: [Freesurfer] question about stats

they are commands included with FreeSurfer. try running the command with --help for usage information and examples On Thu, 14 Jul 2016, Zach Holub wrote: > Awesome. Thanks for the quick reply. What program are those tables in? > > Sent from my iPhone > >> On Jul 14, 2016, at 1:58 PM, Bruce Fisch

Re: [Freesurfer] command line for cp in freeview

you can use -c or --control-points, followed by the path to the contol.dat file. For example: freeview -v subject_name/mri/brainmask.mgz -c subject_name/tmp/control.dat On Thu, 14 Jul 2016, Mihaela Stefan wrote: > Hello Freesurfers, > > What is the command line to load the control.dat file (co

Re: [Freesurfer] Coordinates in TRACULA group analysis

Hi, Anastasia This is trac-all.local-copy from 1 subject. Thank you! Anri ** 京都府立医科大学附属病院 精神科・心療内科 渡辺 杏里 ** Anri WATANABE, M.D. Department of Psychiatry, Univers

Re: [Freesurfer] question about stats

Awesome. Thanks for the quick reply. What program are those tables in? Sent from my iPhone > On Jul 14, 2016, at 1:58 PM, Bruce Fischl wrote: > > Hi Zach > > check out asegstats2table and aparcstats2table and see if they do what you > want > > cheers > Bruce >> On Thu, 14 Jul 2016, Zachariah

[Freesurfer] mpr2mni305 failed

Hi I have run recon-all successfully in the past, but now I am getting an error of mpr2mni305 failed, see transforms/talairach_avi.log. I'm running freesurfer-Darwin-lion-stable-pub-v5.3.0 on a Mac 10.10.5. This issue appears the same as a recent post http://www.mail-archive.com/freesurfer%40n

Re: [Freesurfer] question about stats

Hi Zach check out asegstats2table and aparcstats2table and see if they do what you want cheers Bruce On Thu, 14 Jul 2016, Zachariah Holub wrote: I have run various batches of freesurfer on our MRI scans. Now I want to take many of the stats files from all of our subjects and export them to o

[Freesurfer] question about stats

I have run various batches of freesurfer on our MRI scans. Now I want to take many of the stats files from all of our subjects and export them to one giant excel document. I would like to have a separate sheet for each kind of statistic (i.e. Sheet1=LH aparc.2009a; Sheet2=RH aparc.2009a; Sheet3=

[Freesurfer] FS-FAST "If: Expression Syntax" Error

Hi All, I'm running into an error analyzing some fMRI data with FS-FAST in Freesurfer version 5.3. The analysis runs fine until it gets to the register-sess part, which quits before actually starting to do any registration. The last line of the log file, attached, is "if: Expression syntax", b

[Freesurfer] command line for cp in freeview

Hello Freesurfers, What is the command line to load the control.dat file (control points) in freeview? We tried -cp but it didn't work. Thanks! Mihaela ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/l

Re: [Freesurfer] CVS question

> Date: Thu, 14 Jul 2016 10:35:43 -0400 (EDT) > From: Lilla Zollei > Subject: Re: [Freesurfer] CVS question > To: Freesurfer support list > Message-ID: > > Content-Type: text/plain; charset="utf-8" > > > Hi Michael, > >> I want to compare two populations using CVS so I can cross-regist

[Freesurfer] Fwd: mri_preproc error

-- Forwarded message -- From: YoungHoon Kwon Date: 2016-07-13 21:10 GMT-04:00 Subject: mri_preproc error To: freesurfer@nmr.mgh.harvard.edu Hello FreeSurfer Developers, I tried to assemble the data by using mri_preproc, then it shows segmentation fault (core dumped) after runnin

Re: [Freesurfer] R: problems by running longitudinal mass univariate analysis

Try with the parallel toolbox to speed it up and let me know the warning or error you got. Best, Martin On Jul 14, 2016 4:09 PM, Valsasina Paola wrote: Dear Martin   thank you so much for your answer. Actually, I tried to run the script with the parallel toolbox, but I got some er

Re: [Freesurfer] Hippocampal subfields --> Can\'t find a *ctf file?

The MAC version is now fixed as well. It should be available for download in the next couple of days (Zeke can provide a better estimate). Thanks again to all of you for your feedback. /E Juan Eugenio Iglesias Translational Imaging Group University College London http://www.jeiglesias.com http:/

Re: [Freesurfer] Measuring cortical thickness

Hi Vasudev no, there is no alternative. Computing resources are cheap these days. Most cluster would let you run all your subjects in a single night. cheers Bruce On Thu, 14 Jul 2016, Dev vasu wrote:   Dear Sir / madam, I have 50 subjects (25 healthy controls and 25 patients with BLVP)

[Freesurfer] Measuring cortical thickness

Dear Sir / madam, I have 50 subjects (25 healthy controls and 25 patients with BLVP) , I would like to know how could i generate cortical thickness maps for multi subject group analysis. The initial pre-processing with recon-all takes several hours for single subject, is there any alternate way

Re: [Freesurfer] XQuartz 2.7.9 update results in errors -- possible solution

Hi Zeke, After I created a bugzilla issue, it was identified as a previous issue and they submitted a work around. It has to do with changes made to iglx. See the report: https://bugs.freedesktop.org/show_bug.cgi?id=96260 I’ve NOT tested it

Re: [Freesurfer] CVS question

Hi Michael, I want to compare two populations using CVS so I can cross-register multimodal maps (e.g. ASL, FA, QSM) for volumetric comparisons. I’ve gotten CVS to work very well registering one subject to another, it really is impressive However, using the --mni option, it doesn’t work so w

[Freesurfer] Inquiries about thickness and lgi group analysis

Dear FreeSurfer, I am doing group analysis for thickness and LGI values. I have just got the output and the output of both analyses (sig.mgh file view in Freeview) are exactly the same. Would you please guide me with this? Best Regards, Mahtab. ___ Free

[Freesurfer] R: problems by running longitudinal mass univariate analysis

Dear Martin thank you so much for your answer. Actually, I tried to run the script with the parallel toolbox, but I got some errors and I had to run the version without parallel computing. Anyway, I will run the script till the end and let you know how results look like. The design matrix is re

Re: [Freesurfer] Beta-Zero Correction - No Phase File

If both phase and magnitude data are there, you could use fslroi to separate the images out into two separate files. hth d On 7/14/16 9:52 AM, Afzal, Afsana wrote: > Hi, > > Just wanted to follow up on the issue of just having one fieldmap file > for beta-zero correction outlined below. > > Than

Re: [Freesurfer] Beta-Zero Correction - No Phase File

Hi, Just wanted to follow up on the issue of just having one fieldmap file for beta-zero correction outlined below. Thanks for your help, Afsana __ Afsana Afzal Clinical Research Coordinator Massachusetts General Hospital Division of Neurotherapeutics Department of

Re: [Freesurfer] RB_all_2008-03-26.gca

Hi Gabor how would that be different from just looking at the aseg? cheers Bruce On Thu, 14 Jul 2016, Gabor Perlaki wrote: > Dear all, > > Is it possible somehow to visually inspect the segmentations of the > individual subjects used for the RB_all_2008-03-26.gca atlas? I can extract > the me

[Freesurfer] RB_all_2008-03-26.gca

Dear all, Is it possible somehow to visually inspect the segmentations of the individual subjects used for the RB_all_2008-03-26.gca atlas? I can extract the means, priors and labels, but I am rather interested in the original MRI intensities and labels for the individual subjects. Best Regards,

Re: [Freesurfer] problems by running longitudinal mass univariate analysis

Hi Paola, 1 . It really takes a long time, though I think you probably are missing the parallel toolbox, and running this sequentially will be really slow. 2. You need to wait till the end and look at the percent of places where it did not converge. It is normal that it does not converge in some pl

[Freesurfer] mri_glmfit error

Dear Developers, I am trying to run the mri_glmfit command and I get two different errors for two different subjects. Please find details below. I would be really grateful if you could provide any advice. Error1 setenv SUBJECTS_DIR ./ mri_glmfit --glmdir ./ --y lh.10.lgi.mgh --fsgd fsgd_t

Re: [Freesurfer] Hippocampal subfields --> Can\'t find a *ctf file?

Dear Fernando, Are you using the MAC version? I haven’t finished fixing the bugs in that one yet. If you’re using the Linux version: Zeke, can you please shed some light on what the problem might be? Cheers, Eugenio Juan Eugenio Iglesias Translational Imaging Group University College London ht

[Freesurfer] problems by running longitudinal mass univariate analysis

Dear FS experts I am trying to run the commands for performing the longitudinal mixed effect statistics with the LME Matlab toolbox. I am following the instructions on the web page; however, I have two questions: 1) when I run the command lme_mass_fit_vw, the script is running for a very long t