Freesurfer

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30132 discussions

Postdoctoral Fellow Position at the University of Pittsburgh
by Cat Camacho 15 Mar '18

15 Mar '18

Hello fellow neuroimagers! The Laboratory for Child Brain Development at the University of Pittsburgh is looking for a postdoctoral fellow starting this summer or fall. The LCBD employs multimodal neuroimaging to study child affective development from infancy to middle childhood. Please see the attached ad for more information. Thanks! Cat -- Maria Catalina Camacho PhD Student Center for Neuroscience Laboratory for Child Brain Development University of Pittsburgh mccamacho(a)pitt.edu 512-591-3741

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Skull stripping error dataset
by Matthew Grecsek 15 Mar '18

15 Mar '18

I uploaded the datasets to the ftp site, does anyone have further advice regarding this issue? Both datasets are for the same subject for a longitudinal concussion study and fail for different reasons. matt1 - has "ERROR: GetDICOMInfo(): dcmGetDWIParams() 7 errors" and fails with "CORRECTING DEFECT 51 (vertices=28380, convex hull=5261, v0=32826) XL defect detected..." never completing. matt2 - is leaving out large sections of brain despite various wsthresh adjustments (see thread below) I appreciate any assistance you can provide. All the best, -Matt Hi Matt no idea what that would happen. If you upload the dataset we will take a look cheers Bruce On Mon, 5 Mar 2018, Matthew Grecsek wrote: Following your advice below, it was clearly apparent that the output from the skull stripping step was missing a lot. I tried adjusting the -wsthresh flag from 50 -> 200 and it still left major parts of the brain out. I have a good quality mri and subject with no known anatomical abnormalities. The log file indicates "surface validation has detected possible Error" Does this suggest a more meaningful defect in the base image or something that can be corrected via other parameters or manual editing? Log file attached. Thanks, -Matt Bruce Fischl Fri, 02 Mar 2018 08:00:11 -0800 Hi Matt check the output of the skull stripping. This error usually means that too much (everything?) has been erased and no plausible cc could be found cheers Bruce On Thu, 1 Mar 2018, Matthew Grecsek wrote: My recon-all ended prematurely with the following message: final transformation (x=136.0, yr=-10.054, zr=-0.114): 0.98464 0.00200 -0.17457 15.51372; -0.00197 1.00000 0.00035 17.22442; 0.17457 0.00000 0.98464 -17.83761; 0.00000 0.00000 0.00000 1.00000; mri_cc: no WM voxels found with norm > 40 -- check skull stripping No such file or directory Linux centos-7-1 3.10.0-693.17.1.el7.x86_64 #1 SMP Thu Jan 25 20:13:58 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux recon-all -s matt2 exited with ERRORS at Thu Mar 1 04:35:09 UTC 2018 I am running: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c My full log file is attached. Please let me know suggestions for correcting and continuing the process. Thanks, -Matt

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Re: [Freesurfer] Using .label file as mask in mri_fdr
by Chen Jen-I. 15 Mar '18

15 Mar '18

This is surface-based analysis. I used tksurfer to load the mask.mgh as overlay e.g. tksurfer fsaverage rh inflated -fthresh 2.3 -overlay mask.mgh -delink -curv -gray The mask.mgh file is from the GLMFIT folder after I ran mri_glmfit on my cortical thickness data within the areas set by the label that I have specified Thanks. Jeni Chen Douglas N. Greve<https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=from…> Wed, 14 Mar 2018 15:32:51 -0700<https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=date…> Is this a volume or surface-based analysis? How did you try to visualize it? On Mar 10, 2018, at 12:56 AM, Chen Jen-I. <jen-i.chen(a)umontreal.ca<mailto:jen-i.chen@umontreal.ca>> wrote: Hello, I want to do a FDR correction using mri_fdr within a ROI mask (in .label format). I see the option of passing the sig.mgh volume through a mask, and I read that one can use the mask.mgh in the GLMFIT folder. What is this mask.mgh? I tried to visualize it in Freeview but it doesn’t look like a mask but rather some sort of geometric form. If I have labels as my ROI, how do I convert that into a .mgh format to be used in mri_fdr? (I tried simply using the label file first and obviously that didn’t work…) Thank you in advance, Jeni Chen

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Registering functional data between scan sessions
by David Beeler 15 Mar '18

15 Mar '18

Hi, I have some functional data for the same localizer (dimensions 80x80x38x246) that was acquired in the same subject on two separate days. I would like day 1's raw data to be spatially aligned to the anatomical taken on day 2, but still have the low resolution dimensions of functional space. This question has been asked a couple times before in various forms, but I can't seem to find a clear answer of how to do this correctly. Anatomicals were collected on both days, so I figured I could do something like this: mri_vol2vol --nearest --regheader --mov day1-f.nii.gz --targ $SUBJECTS_DIR/S03/mri/brain.mgz --o day1-f-in-day1-3danat.nii.gz bbregister --s S03_day1 --mov $SUBJECTS_DIR/S03_day2/mri/brain.mgz --reg day1-to-day2.lta --init-fsl --t1 mri_vol2vol --mov $SUBJECTS_DIR/S03_day2/mri/brain.mgz --targ day1-f-in-day1-3danat.nii.gz --o day1-f-in-day2-3danat.nii.gz --reg day1-to-day2.lta --nearest --inv mri_vol2vol --regheader --mov day1-f-in-day2-3danat.nii.gz --targ day2-f.nii.gz --o day1-f-in-day2-func.nii.gz but this is a bad solution because I shouldn't have to actually upsample every time point to high resolution space and then back down again. I figure there must be a way to use the --no-resample flag of mri_vol2vol or something to keep the voxel number (relatively) low and just use the transformation matrix information to go straight from day 1 functional to day 2 functional. Let me know if you have any ideas, thanks! David

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Re: [Freesurfer] running -hippo-subfields with both T1 and T2 using FS 6.0
by Alexopoulos, Dimitrios 15 Mar '18

15 Mar '18

The command below appears to have run successfully but I get a note that the 'volumesAmygdla.txt' file could not be moved. See message below at the end of the freesurfer run. I am using 6.0 (Jan. 18, 2017 release). Is this expected? Jim ----------------------------------------------------------------------- Not resampling, only changing vox2ras matrix To check registration, run: tkregister2 --mov T2inT1space.mgz --targ /data/nil-bluearc/shimony/neonatal/wunder_9_10yo/freesurfer6_0/processed_data/neo321e_fs/mri/norm.mgz --regheader --reg /tmp/reg mri_vol2vol done mv: cannot stat 'volumesAmygdala.txt': No such file or directory Everything done! It took 1921.1425 seconds Started at Wed Mar 14 17:04:06 CDT 2018 Ended at Thu Mar 15 05:35:24 CDT 2018 #@#%# recon-all-run-time-hours 12.522 recon-all -s neo321e_fs finished without error at Thu Mar 15 05:35:24 CDT 2018 done jimalex@linux1% From: freesurfer-bounces(a)nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Iglesias Gonzalez, Eugenio Sent: Tuesday, March 13, 2018 3:22 AM To: freesurfer(a)nmr.mgh.harvard.edu; Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] running -hippo-subfields with both T1 and T2 using FS 6.0 Looks good to me! Sent from my phone, please excuse brevity and typos ________________________________ From: freesurfer-bounces(a)nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu> <freesurfer-bounces(a)nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu>> on behalf of Alexopoulos, Dimitrios <dimitriosalexopoulos(a)wustl.edu<mailto:dimitriosalexopoulos@wustl.edu>> Sent: Tuesday, March 13, 2018 1:06:25 AM To: freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] running -hippo-subfields with both T1 and T2 using FS 6.0 I need a clarification with the command to run for generating the hippo subfields on 6.0 using both a T1 mprage and T2 space (both 1mm isotropic). I'd like to run the entire recon-all -all surface and hippo subfields processing stream. Would this be the correct command: recon-all -s subject -i dicom.dcm -hippocampal-subfields-T1T2 T2.nii.gz T1T2 -all Thanks. Jim ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

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Installation problem
by Neda Mohammadi 15 Mar '18

15 Mar '18

Dear Expert, I tried to install Freesurfer on Ubuntu 16.0.4. I've followed these steps: 1. Download and extract into the directory /usr/local 2.export FREESURFER_HOME=/usr/local/freesurfer Its fine, but when I run this step 3.source $FREESURFER_HOME/SetUpFreeSurfer.sh I receive this message n time -------- freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer FSFAST_HOME /usr/local/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /Work/Processed_data/freesurfer MNI_DIR /usr/local/freesurfer/mni FSL_DIR /usr/share/fsl/5.0 and I must press Ctrl+C to stop. What do I do now? -- *Best Regards,* *Neda*

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lh.volume not found
by Maria Carla Piastra 14 Mar '18

14 Mar '18

Dear Freesurfers, I am running the pipeline described here: http://www.fieldtriptoolbox.org/tutorial/sourcemodel and it fails: mris_convert --volume Subject01_fieldtrip lh /DATA2/results_freesurfer/Subject01/surf/lh.volume MRISread(/DATA2/results_freesurfer/Subject01/surf/lh.white): could not open file No such file or directory when running: /recon-all -finalsurfs -subjid Subject01/ lh.volume does not exist so far. How can I create it? I tried to follow the suggestion here: https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg06716.html, without success. Many thanks, Maria Carla

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Using .label file as mask in mri_fdr
by Chen Jen-I. 14 Mar '18

14 Mar '18

Hello, I want to do a FDR correction using mri_fdr within a ROI mask (in .label format). I see the option of passing the sig.mgh volume through a mask, and I read that one can use the mask.mgh in the GLMFIT folder. What is this mask.mgh? I tried to visualize it in Freeview but it doesn’t look like a mask but rather some sort of geometric form. If I have labels as my ROI, how do I convert that into a .mgh format to be used in mri_fdr? (I tried simply using the label file first and obviously that didn’t work…) Thank you in advance, Jeni Chen

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Report Effect Sizes of Significant Clusters - using .mgh files
by Hannah Claussenius-Kalman 14 Mar '18

14 Mar '18

We used the gamma.mgh and rstd.mgh files to derive an effect size file that we called cohensd.mgh. How can I access these files to report effect size (Cohen's *d*) for significant clusters?

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(no subject)
by Sudeshna 14 Mar '18

14 Mar '18

Hello Freesurfer experts, While doing manual edits, I have had a problem editing the pial surface. When I look at the coronal view of the temporal lobe, the pial boundary does not track properly but the white matter boundary is fine. I have had circumstances where both the pial and white matter boundaries have problems and have been able to correct the issue by editing the white matter. However, in this instance, I am not sure how to fix the problem. Could somebody please tell me how to alter the pial boundary when the white matter boundary is correct? My second issue is a ‘tagging’ issue. While the boundary is correctly drawn, there are little red specks. I am not sure if this is a problem and if so, what I should do to fix it. Thanks in advance, Sudeshna P.S. I have attached some screenshots of the problem described above.

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