Freesurfer May 2018

freesurfer@nmr.mgh.harvard.edu

117 participants
167 discussions

-qcache in recon-all commnd
by Alexopoulos, Dimitrios 07 Jun '18

07 Jun '18

Is it recommended to use the -qcache flag in the basic recon-all -all command? What does it do and what are the advantage of using it? 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.

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creating a mask for the thalamus parcellations
by Erik O'Hanlon 06 Jun '18

06 Jun '18

External Email - Use Caution Dear FS Experts, Is it possible to use the labels found in the FreesurferColourLUT.txt for the Thalamus parcellations (8001-8014) using the mri_extract_label command? If so, what is the correct input file to use ? mri_extract_label <input file????> 8001 L_Ant_thalamus.mgz Thanks Cheers Erik Erik O'Hanlon Postdoctoral researcher [cid:rcsi-crest-signature_f581c185-1d03-45c8-a786-23d8ece3d391.png] RCSI Psychiatry Royal College of Surgeons in Ireland Beaumont Road, Beaumont D9 Ireland T: 8093740 E: erikohanlon(a)rcsi.ie W: www.rcsi.com<http://www.rcsi.com/> Transforming Healthcare Education, Research and Service: RCSI Strategic Plan 2018-2022<http://www.rcsi.ie/strategy2018> RCSI LEADING THE WORLD TO BETTER HEALTH [cid:both3_b9da8717-e91f-4ea7-8729-dc2c4d0a7a5f.png]

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ERROR: mpr2mni305 failed
by Fernanda Hansen P. de Moraes 06 Jun '18

06 Jun '18

External Email - Use Caution Dear FreeSurfer experts, I am having some trouble to understand this error that showed up in some subjects that my group is processing. The recon-all log shows that message: *ERROR: mpr2mni305 failed, see transforms/talairach_avi.log * All talairach_avi.log shows the same error message: *imgrege: no voxels in register ERROR: 'imgreg_4dfp /usr/local/freesurfer/average/711-2C_as_mni_average_305 /usr/local/freesurfer/average/711-2B_as_mni_average_305_mask talsrcimg_g11 none talsrcimg_to_711-2C_as_mni_average_305_t4 3335' failed! status=254 ERROR: mpr2mni305 execution aborted * I believe it happened the same in this thread: *https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg37685.html <https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg37685.html>* but it seems that here the solution is to use .nii images. We are already doing this. Do you have any tip on what to do to solve it? Thank you very much in advance, Fernanda Hansen P. de Moraes -- Fernanda Hansen P. de Moraes Física Médica | Instituto D'Or de Pesquisa e Ensino | Rede D'Or São Luiz

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ROI extraction using functional masks
by Yann Quidé 06 Jun '18

06 Jun '18

Dear FS experts, I am trying to extract values for cortical thickness, surface area and volumes, from different functional ROIs. These cortical ROIs have been defined using SPM tools, and are in .nii format. My scans have been processed using FS v5.3. Although the conversion seems to go well, the “end product” does not really look good, some of the extracted ROI for some subjects are empty. Does anyone have a clue of why? Here is what I have done: 1) transform .nii file to .mgz file $FREESURFER_HOME/bin/mri_convert $MASKS_DIR/ROI.nii $MASKS_DIR/L_ROI.mgz $FREESURFER_HOME/bin/mri_convert $MASKS_DIR/ROI.nii $MASKS_DIR/R_ROI.mgz 2) to make sure our masks from SPM will match fsaverage templates, I did tkmedit -f $MASKS_DIR/avg152T1.mgz -overlay $MASKS_DIR/L_ROI.mgz -fthresh 0.5 tkmedit -f $MASKS_DIR/avg152T1.mgz -overlay $MASKS_DIR/R_ROI.mgz -fthresh 0.5 It was fine. 3) I created a .dat file containing the registration matrix from avg152T1 onto fsaverage cd $SUBJECTS_DIR/fsaverage/surf spmregister --s fsaverage --mov $MASKS_DIR/avg152T1.nii --reg $REG_DIR/avg152T1_to_fsaverage.dat 4) Visualisation of the registration tkregister2 --mov $MASKS_DIR/avg152T1.nii --targ $SUBJECTS_DIR/fsaverage/mri/brainmask.mgz --reg $REG_DIR/avg152T1_to_fsaverage.dat --surf orig The registration was bad, so… I manually relocate the TAL template onto the fsaverage template and saved a new avg152T1_to_fsaverage.dat file called avg152T1_to_fsaverage_edited.dat. This file is used for the next steps. 5) Visualisation of the registration of our mask onto fsaverage T1 cd $SUBJECTS_DIR/fsaverage/surf tkmedit fsaverage T1.mgz \ -overlay $MASKS_DIR/L_ROI.mgz \ -overlay-reg $REG_DIR/avg152T1_to_fsaverage_edited.dat \ -fthresh 0.5 \ -surface lh.white -aux-surface rh.white tkmedit fsaverage T1.mgz \ -overlay $MASKS_DIR/R_ROI.mgz \ -overlay-reg $REG_DIR/avg152T1_to_fsaverage_edited.dat \ -fthresh 0.5 \ -surface lh.white -aux-surface rh.white Up to this sep, everything looks good. 6) Transformation of the ROI mask to surface and thickness mri_vol2surf --src $MASKS_DIR/L_ROI.mgz --reg $REG_DIR/avg152T1_to_fsaverage_edited.dat --hemi lh --o $MASKS_DIR/L_ROI.mgh mri_vol2surf --src $MASKS_DIR/R_ROI.mgz --reg $REG_DIR/avg152T1_to_fsaverage_edited.dat --hemi rh --o $MASKS_DIR/R_ROI.mgh mri_cor2label --i $MASKS_DIR/L_ROI.mgh --surf fsaverage lh --id 1 --l $MASKS_DIR/L_ROI.label mri_cor2label --i $MASKS_DIR/R_ROI.mgh --surf fsaverage rh --id 1 --l $MASKS_DIR/R_ROI.label 7) Extraction of the ROI surface and thickness for analyses mris_anatomical_stats -l $MASKS_DIR/L_ROI.label -f $OUT_DIR/results_L_ROI_SubjID SubjID lh mris_anatomical_stats -l $MASKS_DIR/R_ROI.label -f $OUT_DIR/results_R_ROI_SubjID SubjID rh Thanks to anyone who will be able to help me with that! Yann

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Visualizing Supratentorial volume
by James Gullickson 04 Jun '18

04 Jun '18

External Email - Use Caution All, Is there any way to graphically visualize the segmentations for SupraTentorialVol and SupraTentorialVolNotVent, for example in freeview or tkmedit? Based on the descriptions I have read for the supratentorial values, I want to use them for an analysis. However, I would like to visualize them in my data set for QA purposes to ensure they are capturing what I think they are capturing. Thanks, James

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Subfields Development Version MATLAB:scriptNotAFunction
by Lachlan Strike 01 Jun '18

01 Jun '18

External Email - Use Caution Hi I’m attempting to run the hippocampal/amygdala subfields segmentation in the most recent daily build of FreeSurfer (Centos7). The T1 only and multispectral variations run fine, but attempting the segmentation without the T1 (USE_T1=0) produces the following error: Attempt to execute SCRIPT segmentSubjectT2_autoEstimateAlveusML as a function: /tmp/MCR_3555778206/.mcrCache8.4/segmen0/segmentSubje/segmentSubjectT2_autoEstimateAlveusML.m MATLAB:scriptNotAFunction Error:Attempt to execute SCRIPT segmentSubjectT2_autoEstimateAlveusML as a function: /tmp/MCR_3555778206/.mcrCache8.4/segmen0/segmentSubje/segmentSubjectT2_autoEstimateAlveusML.m Linux vagrant 4.4.0-75-generic #96-Ubuntu SMP Thu Apr 20 09:56:33 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux Any ideas? I am running this within a singularity container, but as the T1 and multispec versions ran without error I’m hoping it’s not related to that. Thanks Lachlan Queensland Brain Institute The University of Queensland, Australia

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Re: [Freesurfer] FSGD design for multi-centre study
by C.P.E. Rollins 01 Jun '18

01 Jun '18

External Email - Use Caution I thought that I could not remove the class since this would mean that the contrast positive and negative values would no longer add up to 0. For instance if I remove only class "patient_centre2_female", then my contrast would have 11 (-1) and 12 (1) as opposed to 12 and 12. Could you please clarify? Thanks again, Colleen -------- Original Message -------- Subject: Re: [Freesurfer] FSGD design for multi-centre study Date: 2018-04-20 11:19 From: "C.P.E. Rollins" <cper2(a)cam.ac.uk> To: Freesurfer <freesurfer(a)nmr.mgh.harvard.edu> Thanks a lot for the explanation. The issue is that I don't think Freesurfer will run a design for which there are no subjects for a given class. So if I keep the classes (24 classes since 6 centres x 2 gender x 2 groups (patient vs. control), and have the contrast with 12 (-1) and 12 (1), -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 1 1 1 1 1 1 1 1 1 1 1 1 0 I get the error: -------------------------------- ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08 -------------------------------- Possible problem with experimental design: Check for duplicate entries and/or lack of range of continuous variables within a class. I'm assuming this is because there are no participants in, for example, patient_centre2_female Is there any way to get around this issue, or should I remove those centres from my analysis (since I can't only remove "patient_centre2_female", as this would make the contrast unbalanced (positives and negatives would not add to the same number). I hope this was clear but please let me know if it was not. Thanks again, Colleen

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white matter and grey matter
by Ritesh Mahajan 01 Jun '18

01 Jun '18

External Email - Use Caution Hello Team, 1) How can i just get the white matter and grey matter together? 2) At what stage of free-surfer i can get this? I tried looking at the brainmask.mgz at the end of recon-all -autorecon1 stage. But, it looks like it has CSF and other parts of brain as well. Can you please help me out with this? Thanks, Ritesh Mahajan

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Cortical thickness and cortical stroke
by Guillaume Bellanger 31 May '18

31 May '18

External Email - Use Caution Hi Freesurfers users, I am looking on cortical thickness after ischemic stroke, especially stroke with cortical involvment. Freesurfer is validated in this population, Li, Q. (2015). When I check the surfaces on Freeview, cortical infarcts are excluded (which is great because of the major anatomy distorsion) but the pial and white surfaces (in contact to the area excluded) are different from zero. It seems that Free-surfer still calculates the cortical thickness as an average measure of the surfaces in contact to the area excluded (which doesn't have any grey matter !). I send you a picture to illustrate my question. I am wondering: how does Freesurfer calculate the surfaces in contact to a cortical area excluded ? If the areas are excluded does it have any consequences on the GLM with QDEC ? Thanks a lot Guillaume

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hippocampal subfield segmentation error (fsv6.0)
by miracle ozzoude 31 May '18

31 May '18

External Email - Use Caution Hello, I am using v6.0 installed on a linux server (via PUTTY) to segment hippocampal subfields. I downloaded the runtime from this link ( https://surfer.nmr.mgh.harvard.edu/fswiki/MatlabRuntime) and followed the instructions on how to install it ( it was installed on the same server as v6.0). The installation process worked fine. However, when I wanted to run recon-all on already processed FS data ( e.g. recon-all -s ${SUBJECTS_DIR}/$session -hippocampal-subfields-T1 -parallel -openmp 6 -bigventricles -3T -time), I encountered an error. I have attached the log for your viewing. Thank you. Best, Miracle

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Freesurfer May 2018