[Freesurfer] Longitudinal proceesing for Pediatric data

Dear freesurfer exports, As it is mentioned in the documentation that 'pediatric data violates the fixed head size assumption' for the current longitudinal stream. Is there any solution for the issue now? Thanks Dong ___ Freesurfer mailing list

Re: [Freesurfer] recon-all error in version 6: MRISread(lh.inflated): could not open file

Oh, sorry for that. I pasted error message below; # #@# Curv .H and .K lh Mon Feb 13 20:27:14 KST 2017 /Applications/freesurfer/subjects/CUBEE0008/surf \n mris_curvature -w lh.white.preaparc \n total integrated curvature = 8.603*4pi (108.105) --> -8

Re: [Freesurfer] Freesurfer v6.0 / Developer version GPU implementation

On 13 February 2017 at 18:15, Francis Tyson Thomas wrote: > I'm trying to reduce the freesurfer runtime as much as possible and I was > wondering if the GPU flags still work for recon-all in Freesurfer v6? If not > is it possible to use the developer version to

[Freesurfer] Postdoctoral Position/Developmental Neuroimaging

The Program for Translational Research on Adversity and Neurodevelopment (P-TRAN) at The Pennsylvania State University is seeking a qualified postdoctoral researcher with expertise in human brain imaging, specifically magnetic resonance imaging (MRI)) with children and adolescents. This position

[Freesurfer] Freesurfer v6.0 / Developer version GPU implementation

Hi, I'm trying to reduce the freesurfer runtime as much as possible and I was wondering if the GPU flags still work for recon-all in Freesurfer v6? If not is it possible to use the developer version to have it running? Also, if I follow the second approach would the results be the same as that

Re: [Freesurfer] Parallelization not working as implemented

What are your execution times? Can you send the recon-all files for your parallel and non-parallel runs? If you run it with -time, then lots of information will be printed to the log for each command. This can be helpful for debugging these types of things. On 02/13/2017 05:13 PM, Francis

Re: [Freesurfer] Parallelization in MAC

I don't know that we have explicitly tested it on a mac, but it should. On 02/13/2017 05:19 PM, Francesco Cardinale wrote: > Dear Freesurfer experts, > Does the parallelization work with Freesurfer 6.0 under MacOS? > Best regards > > Francesco Cardinale, MD > > Neurosurgeon > "Claudio Munari"

[Freesurfer] Parallelization in MAC

Dear Freesurfer experts, Does the parallelization work with Freesurfer 6.0 under MacOS? Best regards Francesco Cardinale, MD Neurosurgeon "Claudio Munari" Centre for Epilepsy and Parkinson Surgery - Ospedale Niguarda "Ca' Granda" Piazza dell'Ospedale Maggiore, 3 - 20162 - Milano - Italia

Re: [Freesurfer] -trac-all -prep FS 5.3 Memory Allocation Issue

That's very strange, it sounds like nothing has changed. Can you please send your trac-all.log file? From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Abigail Waters [awate...@suffolk.edu] Sent: Monday, February

Re: [Freesurfer] -trac-all -prep FS 5.3 Memory Allocation Issue

It's the same. These are all subjects from the same research protocol. From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Yendiki, Anastasia [ayend...@mgh.harvard.edu] Sent: Sunday, February 12, 2017 9:39 PM To:

Re: [Freesurfer] Analysis of rates or percent changes

Hi Katarina, sorry, did not see your previous mail until now. In the future, if you put "longitudinal” somewhere in the subject line, chances are higher that I find it (but not guaranteed either :-) I think using the real time vs using -generic time should give different results in the SPC.

Re: [Freesurfer] hippocampal subfields analysis command

Hi Eugenio, Here are my outputs: ls e009723_FS (one of my subject's freesurfer folder): bem FS1.sh FS2.sh FS4.sh label mri scripts src stats surf tmp touch trash - you can ignore the FS#.sh files - these are matlab script files we run. ls mri/lh.hippoSfVolumes*.txt:

Re: [Freesurfer] hippocampal subfields analysis command

That’s weird. What is the output of the following command? ls /path/to/my/subjects/freesurferfolder And of this one: ls /path/to/my/subjects/freesurferfolder/SUBJECT/mri/lh.hippoSfVolumes*.txt (where SUBJECT is a subject of your choice) Cheers, /Eugenio Juan Eugenio Iglesias ERC Senior

Re: [Freesurfer] Freesurfer Digest, Vol 156, Issue 27

glad it was something easy :) On Mon, 13 Feb 2017, Gronenschild Ed (NP) wrote: Hi Bruce, All output generated is redirected to a temporary log file by me. Fortunately, it is still available and when I look at it I see what happened: it doesn’t find Matlab runtime in the FreeSurferv6

Re: [Freesurfer] Freesurfer Digest, Vol 156, Issue 27

Hi Bruce, All output generated is redirected to a temporary log file by me. Fortunately, it is still available and when I look at it I see what happened: it doesn’t find Matlab runtime in the FreeSurferv6 directory. I’m sorry about this, I just have to copy the MCRv80 from FreeSurferv6b to v6

Re: [Freesurfer] hippocampal subfields analysis command

Hi Eugenio, That's actually the issue, it doesn't generate any file at all.. there's no hippo.txt in the folder where I run it, or in the subject's directory that I had specified. Batool From: freesurfer-boun...@nmr.mgh.harvard.edu

Re: [Freesurfer] Error with mris_anatomical_stats in v6 and high-res data

Hi Ed was there any error message or anything? It just seems to end normally but then gives a nonzero exit code causing recon-all to stop? cheers Bruce On Mon, 13 Feb 2017, Gronenschild Ed (NP) wrote: > Hi, > > All datasets that I've processed sofar with v6 resulted in exactly the same >

[Freesurfer] hippocampal subfields analysis command

Hi, I'm having trouble getting any output from the hippocampal subfield analysis command. I entered in: quantifyHippocampalSubfields.sh T1 hippo.txt /path/to/my/subjects/freesurferfolder I tried both ways of having the environmental variable subjects directory defined to the freesurfer folder

Re: [Freesurfer] hippocampal subfields analysis command

Hi Batool What are the contents of hippo.txt? Just empty? Cheers, /Eugenio Juan Eugenio Iglesias ERC Senior Research Fellow Translational Imaging Group University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/ On 13 Feb 2017, at 16:41, Rizvi, Batool

Re: [Freesurfer] recon-all error in version 6: MRISread(lh.inflated): could not open file

Hi Juhyoung First, can you please paste this kind of thing as text into your email instead of taking snapshots? That makes things easier for us. Second, why are you telling recon-all not to do the inflation with -noinflate2? That is why it can't find the inflated surface. cheers Bruce On

[Freesurfer] Writing FSL compatible ascii files

Dear all knowing list, we are just playing around with the MSM code within FSL and noticed that if we try to convert surface data to ascii like e.g. this mri_convert --ascii funcdata.nii funcdata.asc it produces an ascii file that looks good when opened in a text editor, but doesn't seemt o

[Freesurfer] Coordinates in different modality and space

Dear freesurfer experts, I have some questions about the coordinates conversion, and the relationship between several types of coordinates. First of all, I’d like to confirm whether the coordinates reported in the results summary are based on MNI305 space? Second, I plan to combine