Re: [Freesurfer] recon-all issue {Disarmed}

2017-02-08 Thread Douglas N Greve
can you run the commands below and tell me what happens? cd /home/jamielh/Volumes/Hanson/Pardini_Projects/K_award/10007/surf ln -s lh.white.preaparc.H lh.white.H On 02/08/2017 09:44 AM, Taylor Hilton wrote: > Apologies, that was an old log, attaching the relevant one here. > > > > >> On Feb 7,

Re: [Freesurfer] extract area.pial stats

2017-02-08 Thread Douglas N Greve
You don't need to open it. Just download it and put it in your path. You may want to call it something slightly differnt so that you don't confuse it with the v5.3 version On 02/08/2017 10:53 AM, Clara Kühn wrote: > thanks. What kind of format is it? How do I open it? > > Cheers > Clara > >

Re: [Freesurfer] extract area.pial stats

2017-02-08 Thread Bruce Fischl
try typing: rehash then run it again On Wed, 8 Feb 2017, Clara Kühn wrote: I'm so sorry, I don't know anything about programming... I downloaded it, copied it into my SUBJECTS_DIR as mris_anatomical_stats-doug and tried to run the whole thing again like this: mris_anatomical_stats-doug -mgz

Re: [Freesurfer] extract area.pial stats

2017-02-08 Thread Douglas N Greve
Try this version (same as version 6) https://gate.nmr.mgh.harvard.edu/safelinks/greve/mris_anatomical_stats On 02/08/2017 04:55 AM, Clara Kühn wrote: > Hi Doug, > > thanks for your reply. I tried it out and attached the lh.aparc.pial.stats > file for you to take a look at. As far as I can

Re: [Freesurfer] extract area.pial stats

2017-02-08 Thread Clara Kühn
thanks. What kind of format is it? How do I open it? Cheers Clara - Ursprüngliche Mail - Von: "Douglas N Greve" An: freesurfer@nmr.mgh.harvard.edu Gesendet: Mittwoch, 8. Februar 2017 16:43:47 Betreff: Re: [Freesurfer] extract area.pial stats Try this version

Re: [Freesurfer] Recon-all - finished with errors

2017-02-08 Thread Douglas N Greve
that is bizarre. Can you upload lh.area.mid to our file drop (see end of email) On 02/08/2017 05:21 AM, Bunday, Karen wrote: > Yes, that's it. It just back to the command line after that. > > What do you think the problem is? > > BW > Karen > > Karen Bunday, PhD > Research Associate > Sobell

Re: [Freesurfer] selxavg3-sess: F-contrast but multiple dimension in sig

2017-02-08 Thread Douglas N Greve
if you used the identity matrix then it is the first one On 02/08/2017 08:43 AM, Seung-Goo KIM wrote: > Thank you very much, Doug, > > One more question: so the sig have all T-test results of contrasts > like [1 0 0 … 0], [0 1 0 ... 0], …, [0 0 0 … 1], right? or [1 -1/(N-1) > -1/(N-1), …

[Freesurfer] dcm2niix

2017-02-08 Thread Warner, Graham Cary
Hi all, Can we get dcm2niix added to the system instance of fsl? It can't find it in 5.0.7 or 5.0.9 (please let me know if it is somewhere else and I'm just not seeing it). I'm having problems generating .bval and .bvec files from certain DTI datasets using dcm2nii and the NITRC guys told me I

Re: [Freesurfer] recon-all issue {Disarmed}

2017-02-08 Thread Taylor Hilton
This is the output: ln: failed to create symbolic link 'lh.white.H': Operation not supported > On Feb 8, 2017, at 10:38 AM, Douglas N Greve > wrote: > > can you run the commands below and tell me what happens? > > cd

Re: [Freesurfer] extract area.pial stats

2017-02-08 Thread Clara Kühn
I'm so sorry, I don't know anything about programming... I downloaded it, copied it into my SUBJECTS_DIR as mris_anatomical_stats-doug and tried to run the whole thing again like this: mris_anatomical_stats-doug -mgz -cortex $SUBJECTS_DIR/ZF1K.base/label/lh.cortex.label -f

Re: [Freesurfer] dcm2niix

2017-02-08 Thread Yendiki, Anastasia
Hi Graham – Have you tried mri_convert? The 6.0 version should be able to extract diffusion gradient tables and b-value tables from most standard recent dicoms. a.y From: > on behalf of "Warner, Graham

Re: [Freesurfer] recon-all issue {Disarmed}

2017-02-08 Thread Z K
This error suggests to me that you are mounting some external drive, or docker container, or some mix of file systems incompatible with symlinks? Try moving the subject to a local directory On 02/08/2017 10:41 AM, Taylor Hilton wrote: > This is the output: ln: failed to create symbolic link

Re: [Freesurfer] extract area.pial stats

2017-02-08 Thread Douglas N Greve
It either has to be in your path or you need to supply the full path when running it, like this $SUBJECTS_DIR/mris_anatomical_stats-doug On 02/08/2017 11:27 AM, Clara Kühn wrote: > I'm so sorry, I don't know anything about programming... > I downloaded it, copied it into my SUBJECTS_DIR as

[Freesurfer] Usage of norm.mgz rather than brain.mgz

2017-02-08 Thread Andrew Davis
Hello FreeSurfer Developers, I have been using FreeSurfer for segmenting T1-weighted images, and I have a question related to using the two outputs norm.mgz and brain.mgz. It is my understanding that, by default, FreeSurfer uses the norm.mgz volume to do partial volume weighting when outputting

Re: [Freesurfer] recon-all issue {Disarmed}

2017-02-08 Thread Pål Gunnar Larsson
Hei Dette er en tekstfil i web diskusjonsforum. Det er mange som bruker Freesurfer. Teksten dreier seg om ny lisensfil i samband med en ny versjon. Det aktuelle mailen angår ikke meg. Jeg bruker gammel Freesurfer på jobben som ikke trenger ny lisensfil. Hilsen Pål Dr. philos. Pål G.

Re: [Freesurfer] Usage of norm.mgz rather than brain.mgz

2017-02-08 Thread Bruce Fischl
Hi Andrew the brain.mgz is very aggressively filtered explicitly for cortex and wipes away some subcortical boundaries (e.g. lateral thalamus). cheers Bruce On Wed, 8 Feb 2017, Andrew Davis wrote: Hello FreeSurfer Developers, I have been using FreeSurfer for segmenting T1-weighted

Re: [Freesurfer] extract area.pial stats

2017-02-08 Thread Clara Kühn
Thank you, I think it worked. I've attached the file again. There was one error message in the terminal output though: atlas_icv (eTIV) = 1287829 mm^3(det: 1.512705 ) /nobackup/etsch2/kids/prepost-61kids//ZF1K.base/mri/aseg.presurf.mgz doesn't exist, using old naming conventions Is that

[Freesurfer] FNIRT all NaN's

2017-02-08 Thread Funk, Quentin
Freesurfer experts, I have a few fractional anisotropy images linearly registered to an FA atlas. I'd like to run FNIRT on them with reference the FA Atlas, but when I do, the output is entirely NaNs. I ran the program in verbose mode--and everything is NaN's. e.g.: SSD = -nann = 0

Re: [Freesurfer] extract area.pial stats

2017-02-08 Thread Clara Kühn
alright. Thank you so much! - Ursprüngliche Mail - Von: "Douglas N Greve" An: freesurfer@nmr.mgh.harvard.edu Gesendet: Mittwoch, 8. Februar 2017 17:45:38 Betreff: Re: [Freesurfer] extract area.pial stats No. The program is from version 6 so it is expecting v6

Re: [Freesurfer] FNIRT all NaN's

2017-02-08 Thread Douglas N Greve
Shouldn't you post this to the FSL list? On 02/08/2017 12:17 PM, Funk, Quentin wrote: > > Freesurfer experts, > > > I have a few fractional anisotropy images linearly registered to an FA > atlas. I'd like to run FNIRT on them with reference the FA Atlas, but > when I do, the output is entirely

Re: [Freesurfer] dcm2niix

2017-02-08 Thread Warner, Graham Cary
I just tried it on a few and while it was able to generate the nii files it failed to generate the bval/bvec files I'm looking for. Is it not typical behavior for mri_convert to generate bval/bvec files for DTI runs or is this an error? Graham From:

Re: [Freesurfer] extract area.pial stats

2017-02-08 Thread Douglas N Greve
No. The program is from version 6 so it is expecting v6 naming conventions On 02/08/2017 11:38 AM, Clara Kühn wrote: > Thank you, I think it worked. I've attached the file again. > There was one error message in the terminal output though: > > atlas_icv (eTIV) = 1287829 mm^3(det: 1.512705 )

Re: [Freesurfer] dcm2niix

2017-02-08 Thread Warner, Graham Cary
The set I'm look at now was collected on a GE Signa HDxt. Graham From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Yendiki, Anastasia [ayend...@mgh.harvard.edu] Sent: Wednesday, February 08, 2017 2:09 PM To:

Re: [Freesurfer] dcm2niix

2017-02-08 Thread Antonin Skoch
Dear Graham, you could also try mrconvert of mrtrix3. This tool is very useful and has very good support. http://mrtrix.readthedocs.io/en/latest/reference/commands/mrconvert.html community.mrtrix.org Regards, Antonin Unfortunately I'm not allowed to share these files without direct IRB

Re: [Freesurfer] dcm2niix

2017-02-08 Thread Yendiki, Anastasia
What scanner(s) was it acquired on? From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Warner, Graham Cary [gwar...@mgh.harvard.edu] Sent: Wednesday, February 08, 2017 2:07 PM To: Freesurfer support list Subject:

Re: [Freesurfer] dcm2niix

2017-02-08 Thread Douglas N Greve
Can you upload the dicoms so I can test it out? filedrop address below On 02/08/2017 02:13 PM, Warner, Graham Cary wrote: > The set I'm look at now was collected on a GE Signa HDxt. > > Graham > > *From:*

Re: [Freesurfer] dcm2niix

2017-02-08 Thread Yendiki, Anastasia
Old versions of mri_convert (before 6.0) used to output a default Siemens gradient table - this was not read from the header of the dicom file itself. The 6.0 version reads the table from the header, as long as it is a relatively modern dicom file that has the table in a standard position in

[Freesurfer] LGI using Yeo Atlas

2017-02-08 Thread Martin Juneja
Hi, I used following command to extract LGI values from a set of subjects: recon-all -s -localGI Output stats is saved in lh.aparc_lgi.stats file. By default, its calculating LGI values of 35 areas using *Desikan-Killiany Atlas *but I am interested in calculating LGI values using Yeo atlas of

Re: [Freesurfer] dcm2niix

2017-02-08 Thread Warner, Graham Cary
Unfortunately I'm not allowed to share these files without direct IRB approval (even if they are anonymized). I just tried on some Siemens TrioTim data with the same results. Graham From: freesurfer-boun...@nmr.mgh.harvard.edu

Re: [Freesurfer] dcm2niix

2017-02-08 Thread Warner, Graham Cary
I'm using a large dataset from mi2b2 which contains data from multiple vendors/models collected at different hospitals in the partners network between 2003 and 2016. The data I tried running mri_convert on was acquired in 2011. Graham From:

Re: [Freesurfer] FNIRT all NaN's

2017-02-08 Thread Funk, Quentin
Sent this to the wrong list. Apologies. Quentin Funk, PhD Houston Methodist Research Institute 713-363-9003 From: Funk, Quentin Sent: Wednesday, February 8, 2017 11:17 AM To: freesurfer@nmr.mgh.harvard.edu Subject: FNIRT all NaN's Freesurfer experts, I have

[Freesurfer] ColorLut hippocampus subfields

2017-02-08 Thread Arnaud Boré
Dear Freesurfer developpers, Is there a Freesurfer ColorLut that includes the new subfields of the hippocampus ? In the current colorlut there is no left/right for these subfields: parasubiculum, GC-DG, HATA, molecular layer and tail. In addition, I think it would be easier if the correct

Re: [Freesurfer] recon-all -autorecon2-cp -autorecon-wm -autorecon-pial issue

2017-02-08 Thread 冉倩
Hi Bruce, If I use brain.finalsurfs, then I run recon-all -autorecon2-pial -subjid sub01 or recon-all -autorecon2-pial -autorecon3 -subjid sub01? autorecon3 still need rerunning? Thanks! Best Regards, Qian Ran At 2017-02-08 12:19:35, "Bruce Fischl" wrote:

Re: [Freesurfer] recon-all -autorecon2-cp -autorecon-wm -autorecon-pial issue

2017-02-08 Thread Bruce Fischl
Hi Qian if you just want to regenerate the pial, then yes, edit the brain.finalsurfs.mgz and run: recon-all -autrecon-pial -s -sd note that it is NOT autorecon2-pial, but just autorecon-pial (leave out the '2') cheeers Bruce On Thu, 9 Feb 2017, 冉倩 wrote: Hi Bruce, If I use

Re: [Freesurfer] recon-all -autorecon2-cp -autorecon-wm -autorecon-pial issue

2017-02-08 Thread 冉倩
Hi Bruce, I am a little confused about it. I found 'Manual-Intervention Workflow Directives' on recon-all free surfer wiki web. It said if edits made to correct pial, run-autorecon2-pial. If I only edit pial, I run >recon-all -autrecon-pial -s -sd to fix this issue, I also should rerunning

Re: [Freesurfer] recon-all -autorecon2-cp -autorecon-wm -autorecon-pial issue

2017-02-08 Thread Bruce Fischl
Hi Qian if you look at the recon-all help you will see: USAGE: recon-all Required Arguments: -subjid - Fully-Automated Directive: -all : performs all stages of cortical reconstruction -autorecon-all : same as -all Manual-Intervention Workflow Directives: -autorecon1

Re: [Freesurfer] mrisComputeCorrelationTerm: delta is not finite at vno 0

2017-02-08 Thread Juhyoung Ryu
Yes, I set FREESURFER_HOME variable as '/Applications/freesurfer’, which I installed freesurfer v6. I attached recon-all.log file below. I can see 'build-stamp.txt: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c’ in log file. Is there anything to check more? Thank you, Juhyoung

Re: [Freesurfer] mrisComputeCorrelationTerm: delta is not finite at vno 0

2017-02-08 Thread Bruce Fischl
What does which recon-all return? > On Feb 8, 2017, at 10:54 PM, Juhyoung Ryu wrote: > > Yes, I set FREESURFER_HOME variable as '/Applications/freesurfer’, which I > installed freesurfer v6. > I attached recon-all.log file below. > I can see 'build-stamp.txt:

Re: [Freesurfer] mrisComputeCorrelationTerm: delta is not finite at vno 0

2017-02-08 Thread Juhyoung Ryu
I checked version of recon-all script using 'recon-all -version’ command and 'freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c’ is printed. Juhyoung > On Feb 9, 2017, at 1:02 PM, Bruce Fischl wrote: > > What does > > which recon-all > > return? > >> On Feb 8,

[Freesurfer] PET ROI analysis

2017-02-08 Thread Donatas Sederevicius
?Hello FreeSurfer Developers, I have done partial volume correction of PET data as described in PETSurfer stream. Now, I want to extract a mean intensity value of my ROI for each subject. This ROI is defined in the fsaverage space and saved as a label. What would be the best way to do it?

Re: [Freesurfer] extract area.pial stats

2017-02-08 Thread Clara Kühn
Hi Doug, thanks for your reply. I tried it out and attached the lh.aparc.pial.stats file for you to take a look at. As far as I can tell it's still reporting the white surface area. Or am I reading it wrong? Cheers Clara - Ursprüngliche Mail - Von: "Douglas Greve"

Re: [Freesurfer] Recon-all - finished with errors

2017-02-08 Thread Bunday, Karen
Yes, that's it. It just back to the command line after that. What do you think the problem is? BW Karen Karen Bunday, PhD Research Associate Sobell Department of Motor Neuroscience and Movement Disorders Institute of Neurology, University College London -Original Message- From:

Re: [Freesurfer] selxavg3-sess: F-contrast but multiple dimension in sig

2017-02-08 Thread Seung-Goo KIM
Thank you very much, Doug, One more question: so the sig have all T-test results of contrasts like [1 0 0 … 0], [0 1 0 ... 0], …, [0 0 0 … 1], right? or [1 -1/(N-1) -1/(N-1), … -1/(N-1)] ? Best, -- Seung-Goo KIM > On 2017-02-06, at 18:54, Douglas N Greve wrote: >