Re: [Freesurfer] : cortical thickness ceiling (using an ROI mask)

Hi Kari the average thickness in some ROIs is 5mm??? Like which ones? That certainly seems like something is wrong. Do the surfaces look accurate? What were the parameters/resolution/sequence of the data you gave to recon-all? cheers Bruce On Fri, 3 Jun 2016, Kari Parsons wrote: > Hi, >

Re: [Freesurfer] Coordinates in TRACULA group analysis

Hi, Anastasia. There aren't any .log files but text files like lh.ilf_AS.avg33_mni_bbr.FA_Avg.txt. I guess text files complete all pathways and measures. ** 京都府立医科大学附属病院 精神科・心療内科 渡辺 杏里

[Freesurfer] : cortical thickness ceiling (using an ROI mask)

Hi, I'm using ROI masks (spectroscopy voxels) to get cortical thickness values. I'm pretty much following the tutorial online ('VolumeRoiCorticalThickness') as I'm quite new to Freesurfer. It looks like Freesurfer has a maximum of cortical thickness ceiling at 5 mm, and I'm getting

[Freesurfer] Two functional connectivity methods

Hi FreeSurfer experts, I have two different ways to do functional connectivity, and was wondering which one is optimal since they produce different results. The first is handed down to me from a previous coordinator. However a few of the steps seemed overly complicated, so I looked into a more

Re: [Freesurfer] mri_convert segfault error

Installing the latest version of FreeSurfer has resolved this problem. So as long as the post-processing tools are compatible with these data then I should be fine. Thanks. Josh - Joshua Lee, Ph.D. Post-Doctoral Researcher MIND Institute University of California, Davis 530.747.3805 On Thu, Jun

Re: [Freesurfer] mri_convert segfault error

Maybe its because its not an older version of that file from Ubuntu 12.04. All the data is processed on a different machine, but I then import it on my local machine for running different kinds of analyses (e.g. qdec). Will it matter if I use the latest FreeSurfer version with data processed on

Re: [Freesurfer] mri_convert segfault error

Unfortunately this does not seem to work. locate libcrypt-2 */lib/x86_64-linux-gnu/libcrypt-2.23.so /lib32/libcrypt-2.23.so * cp /lib/x86_64-linux-gnu/libcrypt-2.23.so $FREESURFER_HOME/lib/libcrypt.so.1 [verified it copied, and added to lib

Re: [Freesurfer] mri_glmfit-sim using custom stat outputs

Thanks Doug - so the residual file would be [number of subjects x number of vertices] matrix? Does it have to be in special file format? > So you will generate the sig.mgh file? I would recommend just running > mri_glmfit using a design close to whatever you did to generate the > directory

Re: [Freesurfer] mri_convert segfault error

If you must use 5.1 (I would recommend upgrading), then try what Zeke suggested there. You beat me to the email ;) hth d On Thu, Jun 2, 2016 at 3:41 PM, Joshua Lee wrote: > Perhaps something to do with > > libcrypt-2.*.so ?? > >

Re: [Freesurfer] mri_convert segfault error

Perhaps something to do with libcrypt-2.*.so ?? https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2014-September/040528.html - Joshua Lee, Ph.D. Post-Doctoral Researcher MIND Institute University of California, Davis 530.747.3805 On Thu, Jun 2, 2016 at 12:36 PM, Joshua Lee

Re: [Freesurfer] mri_convert segfault error

I do note that I can enter "freeview ./brain.mgz" and the image opens. Then I can manuall save it as a .nii - Joshua Lee, Ph.D. Post-Doctoral Researcher MIND Institute University of California, Davis 530.747.3805 On Thu, Jun 2, 2016 at 12:33 PM, Joshua Lee wrote: > I had

Re: [Freesurfer] mri_convert segfault error

I had replaced the user name in the output I posted to the listserv for security reasons. I am not on a virtual machine. Fresh install on bare metal. ls -l ../ ... > drwxr-xr-x 13 myuser myuser 4096 Jun 2 11:50 mri > ... > > - Joshua Lee, Ph.D. Post-Doctoral Researcher MIND Institute University

Re: [Freesurfer] mri_convert segfault error

Hi Doug, Yes the quoted lines were output fromt her terminal. ls -l brain.mgz > -rwxrwx--- 1 myuser myuser 1216430 May 18 17:06 brain.mgz > I have many Tb of disk space. I can chmod 777 the files and still seg faults. Thanks Josh - Joshua Lee, Ph.D. Post-Doctoral Researcher MIND Institute

Re: [Freesurfer] mri_convert segfault error

Can you send the full terminal output? Or is that it? Do you have enough disc space or is it running out? what is the result of ls -l brain.mgz On 06/02/2016 03:07 PM, Joshua Lee wrote: > On freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 installed on > Ubuntu 16.04 LTS > mri_convert is seg

Re: [Freesurfer] mri_glmfit-sim using custom stat outputs

So you will generate the sig.mgh file? I would recommend just running mri_glmfit using a design close to whatever you did to generate the directory structure, then just replace the sig.mgh file with the file of your choosing. The one snag may be the fwhm.dat file. This is a measure of the

[Freesurfer] mri_convert segfault error

On freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 installed on Ubuntu 16.04 LTS mri_convert is seg faulting >>ls brain* > brain.finalsurfs.mgz brainmask.auto.mgz brainmask.mgz brain.mgz > > mri_convert ./brain.mgz --in_type mgz --out_type nii -o ./brain.nii > > $Id: mri_convert.c,v

[Freesurfer] mri_glmfit-sim using custom stat outputs

Dear experts, This is a follow-up question from my previous post. http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg47287.html If I am running stats with my own stats code to generate p-values and other parameters, what other files do I need to generate in order to run

Re: [Freesurfer] correlation with glm

that is the right contrast. You can use that or divide by 6 (you have 6 groups). The significance will be the same regardless of of scale, it will only make a difference if you try to interpret the gamma.mgh file On 06/02/2016 12:06 PM, Clara Kühn wrote: > I have and it's been very helpful. I'm

Re: [Freesurfer] epidewarp.fsl radian phase range error

Where did you read that? I've put the the latest and greatest here: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/epidewarp.fsl On 06/02/2016 09:20 AM, Milde, Christopher wrote: > > Dear FS experts, > > I also encountered this problem when trying to apply epidewarp.fsl: > > ERROR:

Re: [Freesurfer] Brainmask edit error

Hi Sabrina, I'm not entirely sure about that, but if my manual edits don't work I'll let Bruce know and we can discuss other workarounds. -Ani On 06/02/2016 12:55 PM, Sabrina Yu wrote: Hi Ani, Thanks so much for your explanation, it makes sense that the brain is too deformed for one

Re: [Freesurfer] Downsampling data and writing mgh file

You'd have to issue multiple mri_surf2surf commands and then run mri_concat on all the output files to give you a stack in one file. Alternatively, you can ues mris_preproc with --targ fsaverage6 On 06/02/2016 01:20 PM, Nandita Vijayakumar wrote: > Dear FreeSurfer Experts, > > I'm trying to

Re: [Freesurfer] Brainmask edit error

Hi Sabrina, Usually we don't add voxels in the brainmask. We usually add to the wm.mgz which pushes the white surf out and ultimately the pial surf out (because it grows from the white). If the area around the stroke on both sides looks good but there is a hole in the middle where there is no

Re: [Freesurfer] correlation with glm

I have and it's been very helpful. I'm not sure though where a correlation was specified in those examples. If I understand it correctly, I have to set my groups to 0 and my covariate to 1. The columns in my designamtrix look like this: 1male 1female 2male 2female 3male 3female 1male_behavior

Re: [Freesurfer] About TRACULA

Hi Yang - TRACULA does not assume that the shape, size, or integrity of the tracts is the same in the study subjects as in the atlas subjects. It just assumes that the relative position of the tracts with respect to the cortical and subcortical segmentation labels from freesurfer. For

Re: [Freesurfer] About TRACULA

Hi, To be specific, I'm trying to reconstruct arcuate fasciculus (refer to SLFT according to your paper 2011) in patients who suffered from frontal or temporal or parietal gliomas. I noticed that TRACULA was used to study neuropsychiatry and neurodegeneration diseases, such as

[Freesurfer] epidewarp.fsl radian phase range error

Dear FS experts, I also encountered this problem when trying to apply epidewarp.fsl: ERROR: input phase image exceeds allowable phase range. Allowable range is 6.283 radians. Image range is: 12.5633 radians I read that there is an updated version of epidewarp.fsl which might solve this

Re: [Freesurfer] correct thinking?

it would be in your statistical analysis. It's not that they aren't reliabile, it's that the correlation of volume with overall size of the intracranial vault is typically not that interesting and regressing it out makes you more sensitive to e.g. disease effects On Thu, 2 Jun 2016, Marja

Re: [Freesurfer] Selxavg3-sess with no-con-ok and ROI analyses

That's my bad. I tried with selxavg3-sess and I get a different error saying no contrasts and to create contrasts with mkcontrast-sess or run with -no-con-ok. Is it possible I did mkanalysis-sess wrong? Thanks! Talia From:

Re: [Freesurfer] Brainmask edit error

Hi Ani, Thanks for looking into this for me. I'm actually out of town right now, so cannot access the subject in front of me. Yes, it is. As I am trying to generate the stats on intensity over an ROI, I am hoping to be able to generate good surfaces. To me, the aseg looks pretty good. The

Re: [Freesurfer] correct thinking?

Just out of curiosity, if I want to include subcortical volumes, how would I include ICT as a regressor? And why do you need to include it while the normal recon -all -all already provides us with subcortical volumes? (are they not reliable enough?) Best, Marja On Thu, Jun 2, 2016 at 9:29 PM,

Re: [Freesurfer] correct thinking?

Sorry, ICV (intracranial volume) > On Jun 2, 2016, at 4:40 AM, John Epiktitos wrote: > > Hello, > What is ICT ? > Thanx > >> On Jun 1, 2016 4:21 PM, "Marja Caverlé" wrote: >> Hi Bruce, >> >> Thanks for your answer and all your help, I only want

Re: [Freesurfer] About TRACULA

Hi - It's hard to predict in advance what will happen without trying it out. A lot will depend on the size/position/nature of the tumor. Some tumor patients will go through just fine, other will have issues. If the freesurfer segmentation works, then tracula will work too. Best, a.y On

[Freesurfer] Postdoctoral position in computational neuroimaging

Postdoctoral position in computational neuroimaging The Child and Adolescent Psychiatry at Ludwig Maximilian University (LMU) Munich is looking for a postdoctoral candidate in computational neuroimaging. The researcher will be involved in the development of new algorithms for the analysis of

Re: [Freesurfer] correct thinking?

Hello, What is ICT ? Thanx On Jun 1, 2016 4:21 PM, "Marja Caverlé" wrote: > Hi Bruce, > > Thanks for your answer and all your help, I only want to look at cortical > thickness for now. > > Best, > > Marja > > On Wed, Jun 1, 2016 at 11:11 PM, Bruce Fischl

Re: [Freesurfer] Questions about fsgd file & contrast

Thank you. Is the following setup looks correct? We have 1 group of subjects, half came at TP1 & TP2, half came at TP1 & TP3. And we would like to do a Two Stage longitudinal anaylsis later, is it correct if we put in the following way? *GroupDescriptorFile 1 **Title G2V2 * *Class