Re: [Freesurfer] correlations with longitudinal data

Hi Martin, thanks for your reply. I have created a qdec file with the fsidtp1.long.fsid.base as first column and specified the long directories with /path_to_data/*.long.*. And each subject has a ?h.thickness file from the recon-process. However, Qdec is asking for a very specific file

Re: [Freesurfer] FreeSurfer 6 recon-all exiting with errors at -cortparc step

HI Natalia can you try the dev version? I'm pretty sure I fixed this. You can just rerun mris_ca_label. We'll hopefully be cutting a new stable 6 sometime soon cheers Bruce On Wed, 9 Dec 2015, Zaretskaya, Natalia wrote: Dear all, I am running recon-all with FreeSurfer 6 stable version

Re: [Freesurfer] Recon-all get stucked without error during processing

Hi Matthieu you need to track backwards and see where the problem started. Why is the norm warped? Actaully, it shouldn't be warped, although it might be truncated if the skull stripping failed. cheers Bruce On Wed, 9 Dec 2015, Matthieu Vanhoutte wrote: Hi Bruce, Indeed norm.mgz isn't

Re: [Freesurfer] ERROR: Talairach QA check failed! and ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED***

Hi Bruce, I tried to follow the tutorial : http://freesurfer.net/fswiki/FsTutorial/Talairach_freeview But nothing appeared in the image window of tkregister2 command... Below you'll find the log of the command : tkregister2 --mgz --s M0_2010-03-25 --fstal tkregister_tcl

Re: [Freesurfer] Recon-all get stucked without error during processing

Hi Matthieu this might be a bug that is fixed in 6.0. Can you cehck the input to mri_cc (norm.mgz) and make sure it is not empty? In older versions if the skull stripping failed and generated an empty norm.mgz/aseg.auto_noCCseg.mgz the mri_cc code would hang. cheers Bruce On Wed, 9 Dec 2015,

[Freesurfer] file error

OS Opensuse 13.2 Freesurfer 6 Dev Logfile Attached I have had no luck trying to get freesurfer to run. It is failing at the same point each time ( Please see log). I have tried with multiple datasets in multiple locations both on the local machine and across the network. I have also

[Freesurfer] Qdec - cluster labels

Hi all - When you get a significant cluster after doing monte-carlo simulation, we get peak vertex/Talairach coordinates and also saved in *summary files. Is there a way to find all the parcellated regions (Desikan, or, Destriuex) in the significant clusters? Thanks,Sabin

Re: [Freesurfer] Recon-all get stucked without error during processing

Hi Bruce, Indeed norm.mgz isn't empty but doesn't look well (truncated and warped). Is this bug fixed in the v6 beta release ? If this is the case : 1) Would you advise me to try on the v6 ? 2) Should I so relaunch all recon-all process on my subjects computed with v5.3 and work only with the

Re: [Freesurfer] Recon-all get stucked without error during processing

Hi Bruce, In fact T1.mgz is ok, but the skull stripping failed and seemed to have taken only the jawbone and the neck. Best regards, Matthieu 2015-12-09 16:16 GMT+01:00 Bruce Fischl : > Hi Matthieu > > you need to track backwards and see where the problem started.

Re: [Freesurfer] Edit the number of segments in the segmentation of the corpus callosum

Hi Doug, Hi Bruce, Just an update. I tried this command (see below) to specify each input file since I don't want to freesurfer to choose the stats/aseg.stats that it uses by default. but I get this "ERROR: The stats file e0042/stats/e0042_CC12_new.aseg.stats is not found or is too small to be

Re: [Freesurfer] Question about Qdec

Hi Doug, Thank you for letting me know. 1) machine being used: Linux localhost.localdomain 3.10.0-229.4.2.el7.x86_64 #1 SMP Wed May 13 10:06:09 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux 2) Freesurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0-HCP 3) Current working directory:

Re: [Freesurfer] selxavg3-sess ERROR

hi doug, thank you so much for your quick reply. yes - I saw this error after I sent you the error log. I checked the paradigm file, corrected it and rerun everything. now this error is gone but I still get the following: Error using svd Input to SVD must not contain NaN or Inf. Error in cond

Re: [Freesurfer] selxavg3-sess ERROR

That means that your design matrix is ill-conditioned. This error means one of two things is wrong with your .par file (located in each run of each subject’s bold directory): 1) there are not two or more occurrences of one of your conditions; or 2) there is a pattern to your conditions (for

Re: [Freesurfer] selxavg3-sess ERROR

Did you see the error description: ERROR: /space/mdeh5/1/halgdev/projects/christina/FSFAST/Project/NC211_fmri_060515/Sess01/bold/004/oddeven.par is not correctly formatted. Line 19 only has 0 items did you check this file? On 12/09/2015 12:38 PM, Christina Pressl wrote: > Dear Freesurfer

[Freesurfer] Qdec questions

Hi all - When you get a significant cluster after doing monte-carlo simulation, we get peak vertex/Talairach coordinates and also saved in *summary files. Is there a way to find all the parcellated regions (Desikan, or, Destriuex) in the significant clusters? Thanks

Re: [Freesurfer] May you help me with 'recon-all' errors

Hi Peng nifti should be fine as input, but definitely don't use analyze. It doesn't preserve the direction cosines so once you convert to it you will never be sure which side of the image is the left hemim and which is the right. I can't help with the 'can't locate MNI/Startup.pm ' error.

[Freesurfer] Processing macaque data

Dear Experts, I am trying to modify the HCP pipeline scripts to work with macaque data (in vivo, 0.5mm isotropic). The Pipeline uses FSL and a FreeSurfer. In FreeSurferPipeline.sh there are some steps I'm not sure how to modify them to work correctly with macaque data instead of the human data:

Re: [Freesurfer] May you help me with 'recon-all' errors

Thank you! Hopefully, I can either figure it out myself or be helped by someone. Thanks! Best, Peng On Wednesday, December 9, 2015, Bruce Fischl wrote: > Hi Peng > > nifti should be fine as input, but definitely don't use analyze. It > doesn't preserve the

Re: [Freesurfer] May you help me with 'recon-all' errors

Hi Peng it looks like we can't read your input dicom. For example, the log says: reading from /Users/Peng/Documents/MNE/MNE_analysis/MRI/R2261_S0283/m000-gm_A0136_N12518_S0283_20120817_P5716_averageCBF_normalized.dcm... Starting DICOMRead2() dcmfile =

[Freesurfer] Brainstem Substructures in Freesurfer 6.0 - how to calculate left/right volumes

Hello, I've installed Freesurfer 6.0 beta, and run the -brainstem-structures option to recon-all. The results look ok, but I'd like the left/right volumes for the superior cerebellar peduncle (SCP), rather than the total volume. Is there any easy way to do this? Thanks, Chris

[Freesurfer] May you help me with 'recon-all' errors

Dear freesurfer expert, I am a student from University of Maryland, learning freesurfer for MNE analysis recently. I have a perhaps silly problem and could not solve by myself. The problem occurred as 'recon-all -s R2261_S0283 exited with errors...' when I was running 'recon-all -autorecon-all

Re: [Freesurfer] selxavg3-sess ERROR

I see, here is a copy of my paradigm 0. 2 11.100 0 21.100 3 32.200 0 42.200 2 53.300 0 63.300 2 74.400 0 84.400 1 95.500 0 105.500 1 116.600 0 126.600 3 137.700 0 147.700 3 158.800 0 168.800 1 179.900 0 I don’t see how this setup reflects one of the two potential errors you outlined.

[Freesurfer] Minc File Error

Zeke and others, I recently installed Freesurfer v6 ( freesurfer-Darwin-OSX-stable-v6-beta-20151015.dmg , MacOS 10.9.5, XQuartz 2.7.8), and Freeview always closes whenever I try to

[Freesurfer] selxavg3-sess ERROR

Dear Freesurfer Experts, I am having trouble with selxavg3-sess and was wondering if you could maybe help me resolving the issue (error log attached) I ran #preproc-sess –s Sess01 –surface fsaverage lhrh –mni305 –fwhm 5 –per-run and the following commands for lh, rh and mni305