Freesurfer February 2021

freesurfer@nmr.mgh.harvard.edu

98 participants
118 discussions

Re: [Freesurfer] Missed Module nibabel Python -- Re: Form submission from: Infant Freesurfer Download Request
by Zollei, Lilla,Ph.D. 11 Feb '21

11 Feb '21

Hi Sair, Just to make sure, could you run? fspython -m pip install nibabel Otherwise you can re-install the distribution as we have update the latest one with the missing nibabel package. Best, Lilla ________________________________ From: Carlos Sair Flores Bautista <sairfb(a)inb.unam.mx> Sent: Wednesday, February 10, 2021 8:52 PM To: Zollei, Lilla,Ph.D. <LZOLLEI(a)mgh.harvard.edu> Cc: freesurfer(a)nmr.mgh.harvard.edu <freesurfer(a)nmr.mgh.harvard.edu> Subject: Missed Module nibabel Python -- Re: Form submission from: Infant Freesurfer Download Request External Email - Use Caution Hello Freesurfer Team My Name is Sair, i have been trying to run a test subject on last dev version of freesurfer infant pipeline, however when i try to run this subject i receive the next error from infant recon all process: Reslicing using trilinear interpolation writing to /home/lain/Documents/PruebasFsInfant/test/work/mprage.nu.conf.nii.gz... CONFORMED FILE /home/lain/Documents/PruebasFsInfant/test/work/mprage.nu.conf.nii.gz Traceback (most recent call last): File "/usr/local/freesurferinfant/python/scripts/sscnn_skullstrip", line 5, in <module> import nibabel as nib ModuleNotFoundError: No module named 'nibabel' it suppose the last freesurfer infant dev version contains python 3.6 however i have made sure to check the availability of this module on the installed python version however this still happens every time, also i have made the same test on different server and pc getting the same error. i have tested it on debian and ubuntu I have attached to this mail the complete stream from my infant recon all test in order to analyze and help to receive support from your side. thanks in advance. Best regards Sair. L.C.E. Carlos Sair Flores Bautista Secretario Tecnico INB-UNAM El mié, 13 de ene. de 2021 a la(s) 15:24, Zollei, Lilla,Ph.D. (LZOLLEI(a)mgh.harvard.edu<mailto:LZOLLEI@mgh.harvard.edu>) escribió: Thank you for your interest in the infantFreesurfer pipeline. The version below is our new beta distribution (Jan 2021). Please, continue giving me feedback and asking a lot of questions along the way so that we can improve upon the user-friendliness of its use. After downloading the package, you should run the below four commands: source YOUR_FREESURFER_ENVIRONMENT setenv SUBJECTS_DIR your_data_path or export SUBJECTS_DIR=your_data_path infant_recon_all --s SUBJ --age age_in_months SUBJ is the subjectID of the subjects's whose data you are processing. The script will expect the input file to be located at $SUBJECTS_DIR/$subj/mprage.nii.gz or $SUBJECTS_DIR/ $subj/mprage.mgz by default. Unless otherwise specified, the output of this process will be saved to $SUBJECTS_DIR/$SUBJ using a FreeSurfer type directory structure. If the --masked flag is used, we recommend also running intensity normalization, for example by using: mri_nu_correct.mni --i $infile --o $nufile --n 2 Note, you can use both tcsh and bash for this distribution. Before execution, you will also need install FSL [https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FslInstallation<https://secure-web.cisco.com/1cGp1eiz_7sOm02QhOvn3jmhR4tJTNPCAhjpNXJy9K5rBP…>]. Note, we have changed our default nonlinear registration tool. We rely on niftyreg which ships directly with this release. If you would like to use DRAMMS you will need to install it separately and use the corresponding flag. Other useful flags: --outdir (redirecting output) --kneigh (number of training examples to use) See infant_recon_all --help for more information or visit https://surfer.nmr.mgh.harvard.edu/fswiki/infantFS<https://secure-web.cisco.com/1SO4Xs7x3V6qnRb_RWiJBY343GLDSD6_eDDvRSlrhuC-wT…> * Skullstripping The current release ships with our new skullstripping tool so you will not need to skullstrip your data before running infantFS. Note, the new tool requires about 23GB of memory! At present, the error messages related to lack of sufficient memory are pretty vague, so please, check whether you have enough if you rely on this tool. Also "Your CPU supports instructions that this TensorFlow binary was not compiled to use" is just a warning not an error. It indicates that the process could be faster if you built with a more modern tensorflow, but the computations should be working even with this version. * Citation: Cite the below papers if you use our work and publish yourself: Zöllei, L, Iglesias, JE, Ou, Y, Grant, PR, Fischl,B. Infant FreeSurfer: An automated segmentation and surface extraction pipeline for T1-weighted neuroimaging data of infants 0-2 years, NeuroImage, Volume 218, September 2020, 116946 https://doi.org/10.1016/j.neuroimage.2020.116946<https://secure-web.cisco.com/1QyTKPVjpukeljrh0n5fRo7K-S_AxdepVjCQ_yydZp7OgY…>. (http://www.sciencedirect.com/science/article/pii/S1053811920304328<http://secure-web.cisco.com/124O1IxeSlJOGHpA_Mg0Tx1tyLZSHjY4vKxlkhb2cRAzqZw…>) de Macedo Rodrigues, K., et al., A FreeSurfer-compliant consistent manual segmentation of infant brains spanning the 0–2 year age range. Front. Hum. Neurosci., 2015. 9(21). * Download: https://surfer.nmr.mgh.harvard.edu/ftp/dist/freesurfer/infant/freesurfer-li…<https://secure-web.cisco.com/1tBEYaGAdDitkfPUajg7pJGKaxxzO-KQ7FVRcE-R55wnSj…> Lilla NOTE: Currently, the parcellation information (aparc) is provided only for the sake of completeness but has not been fully validated. It is a projected version of the adult atlas, so it does not originate from the infant training data set directly! ________________________________ From: webmaster(a)nmr.mgh.harvard.edu<mailto:webmaster@nmr.mgh.harvard.edu> <webmaster(a)nmr.mgh.harvard.edu<mailto:webmaster@nmr.mgh.harvard.edu>> on behalf of MGH/HST Martinos Center for Biomedical Imaging via MGH/HST Martinos Center for Biomedical Imaging <webmaster(a)nmr.mgh.harvard.edu<mailto:webmaster@nmr.mgh.harvard.edu>> Sent: Thursday, January 7, 2021 10:12 AM To: lzollei(a)nmr.mgh.harvard.edu<mailto:lzollei@nmr.mgh.harvard.edu> <lzollei(a)nmr.mgh.harvard.edu<mailto:lzollei@nmr.mgh.harvard.edu>> Subject: Form submission from: Infant Freesurfer Download Request Submitted on Thursday, January 7, 2021 - 10:12 Submitted by anonymous user: 189.128.48.80 Submitted values are: Name: Carlos Sair Flores Bautista Email Address: sairfb(a)inb.unam.mx<mailto:sairfb@inb.unam.mx> Institution: UNAM-México Operating System Used: Debian Intended use of the Pipeline: analyze the neurodevelopment between perinatal brain damage subject dataset and control subject data set during 0-8 years in a longitudinal analysis The results of this submission may be viewed at: https://www.nmr.mgh.harvard.edu/node/8319/submission/31809<https://secure-web.cisco.com/1ZLBHTi_QZ1M8KoGgrzKvLFWXqE6-zLjpsABpjUgPA4ubT…> The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at http://www.massgeneralbrigham.org/complianceline<http://secure-web.cisco.com/1ND4Et7v64GxG61i6JVC2kcSsAjoYmzPSdgk95vYUnxp3oh…> . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

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Permission to create directory denied
by Gabriel Mackie 11 Feb '21

11 Feb '21

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SAMSEG for Alzheimer´s Disease study
by Steve Petersen 10 Feb '21

10 Feb '21

External Email - Use Caution Dear Freesurfer experts, We are working with a large MRI dataset (FLAIR, T1) of healthy adults and adults with mild cognitive impairment. Can we use SAMSEG to segment white matter lesions in this population?. Thanks for your help! Best, Steve.

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Re: [Freesurfer] error in running tkregisterfv
by Takahiko Kawashima 10 Feb '21

10 Feb '21

External Email - Use Caution Hello Peter, This thread was made 3 months ago, but I post additional information here. Hope it will help anyone who meets the same issue. My environment is almost same as yours (FS ver. 7.1 on macOS Mojave), and I experienced the same error. Version of bash seems the cause. The “-v” option of “test” command in bash is implemented in bash later than ver. 4.2. Indeed I could solve the issue by installing newer bash. Please don’t forget to change shebang of fsvglrun if you install new bash in other path than /bin/bash! Best regards, Takahiko > On 12/20/2020 5:03 AM, Peter de Best wrote: > External Email - Use Caution > What am I trying to do: > I am trying to register my functional resting state scan to the MPRAGE scan > (which is saved in the freesurfer subjects directory under ‘subject_30_8_2020’ > after running recon-al on a MPRAGE that was aligned to AC PC). The mgz file > brain.mgz and the functional scan aligned. > What are the commands I use > bbregister --s subject_30_8_2020 --mov > subject_motion_corrected_func_4D_RestingState.nii --reg > affine_TESTTESTTEST6July2337_1_matrix_AVERAGE.dat --init-header –bold > tkregisterfv --mov subject_motion_corrected_func_4D_RestingState.nii --reg > affine_TESTTESTTEST6July2337_1_matrix_AVERAGEbbb.dat –surfs > (bbregister works, tkregisterfv does not; I only provide the bbregistercode for > context) > What is the error? > When I try to run tkregisterfv, I get the following output: > “cd /Users/me/Documents/30_8_2020/subject_REST_CF > freeview -transform-volume -viewport cor -v > /Applications/freesurfer/7.1.1/subjects/subject_30_8_2020/mri/orig.mgz:visible=0:name=orig.mgz(targ)/Users/me/Documents/30_8_2020/subject_REST_CF/subject_motion_corrected_func_4D_RestingState.nii:name=subject_motion_corrected_func_4D_RestingState.nii(mov):reg=/Users/me/Documents/30_8_2020/subject_REST_CF/affine_TESTTESTTEST6July2337_1_matrix_AVERAGEbbb.dat > --surface > /Applications/freesurfer/7.1.1/subjects/subject_30_8_2020/surf/lh.white:edgecolor=yellow--surface > /Applications/freesurfer/7.1.1/subjects/subject_30_8_2020/surf/rh.white:edgecolor=yellow > /Applications/freesurfer/7.1.1/bin/fsvglrun: line 20: conditional binary > operator expected > /Applications/freesurfer/7.1.1/bin/fsvglrun: line 20: syntax error near > `FS_ALLOW_VGLRUN' > /Applications/freesurfer/7.1.1/bin/fsvglrun: line 20: `if [[ ! -v > FS_ALLOW_VGLRUN ]]; then'” > My platform: > macOS Mojave, version 10.14.6 > There is no recon-al log. > What I tried to do/ checked: > 1) FSL is installed. > 2) the fsvglrun text describes fsvgl as a necessary file, and I found that > VirtualGL is supposed to contained that, and I tried to install that. It also > says that FS_ALLOW_VGLRUN should be set to 1, but I have no idea how to do that. > 3) make sure to reboot after every potential solution. > None of that worked/ resolved the issue. > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> > https://secure-web.cisco.com/1mghbRbdQp2NBhEK9y-ocIdgx-Br8K0MGsdp5VagBN8Xk2… > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://secure-web.cisco.com/1mghbRbdQp2NBhEK9y-ocIdgx-Br8K0MGsdp5VagBN8Xk2…

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non-pvc processing error
by miracle ozzoude 09 Feb '21

09 Feb '21

External Email - Use Caution Hi Doug, I followed the processing workflow as described on the PETSurfer wiki and gtmseg.mgz was created, but included a warning for only one of my subjects: WARNING: segid 29 Left-undetermined tissue type is not set Writing output file to /ID/mri/gtmseg.mgz Writing colortable to /ID/mri/gtmseg.ctab Writing lta file to /ID/mri/gtmseg.lta Next, I ran both pvc and non-pvc. However, the non-pvc failed, whereas the pvc did not. These are the commands I ran and the error I got for non-pvc: mri_gtmpvc --i /input.nii.gz --reg PET.lta --psf 0 --no-tfe --seg gtmseg.mgz --default-seg-merge --auto-mask PSF 0.01 --mgx 0.01 --o /gtmnopvc.output.ref --rescale 8 47 vgthresh 0.001000 nReplace 18 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 24 avail.processors, using 1 Creating output directory /gtmnopvc.output.ref Loading seg for gtm /ID/mri/gtmseg.mgz Loading seg ctab /ID/mri/gtmseg.ctab Reading /ID/mri/gtmseg.lta Replacing 18 Pruning ctab Checking tissue type ERROR: CheckSegTissueType() tissue type for seg 29 Left-undetermined not set Failed tissue type check Also , in the aux folder of non-pvc, only limited amount of files were created, including: Mask.nii, seg.ctab, seg.nii, seg.replace.list, seg.vol.nii Any idea why only the non-pvc failed ? Any help would be greatly appreciated! Many thanks

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Issue with Segmentation
by Katherine Andrade 09 Feb '21

09 Feb '21

External Email - Use Caution To whom this may concern, I've been running segmentation for over 100 hours and I'm not entirely sure how to fix this issue. Is this the right address to ask for help? Best, Katie

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Different sequences
by Alp Karakaşlı 09 Feb '21

09 Feb '21

External Email - Use Caution Hello, We are working with a large number of acquired imaging and unfortunately, the pulse sequences that have been used are not the same. We have two different groups of pulse sequence: T1-3D-FFE and T1-MPRAGE. Could we use all of these images in the same study? Thank you in advance for your answer, A. Alp Karakasli Hitit University Department of Psychiatry

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Group Analysis
by Larissa Bechtle 09 Feb '21

09 Feb '21

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vascular damage meassures
by Alberto Del Cerro Leon 09 Feb '21

09 Feb '21

External Email - Use Caution Hello Freesurfer, my lab is interested in measuring the vascular damage in different subjects. I read that Freesurfer can measure the hypointesities characteristic of brain damage in an automated way. However I couldn't find the properly workflow to do that Someone could help us?

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Covariates
by Magdalena Banwinkler 09 Feb '21

09 Feb '21

External Email - Use Caution Dear Freesurfer experts, We are investigating brain structure differences between 2 groups. We are using Gray Matter Volume and Cortical Surface Area as structural measures and want to look at specific ROIs. We want to include Sex, Age and TIV as covariates. However, we are unsure if we should correct for TIV when using Cortical Surface Area or only when using Gray Matter Volume. We would be very happy about any kind of help or literature regarding this question! Additionally, we have calculated a whole brain GLM analysis and found significant differences between groups. After inclusion of covariates, no result remained significant. However, when using an ROI approach including the same covariates, the results strongly indicated between group differences. Does anyone have an idea on why this could be the case? Thank you very much for your help! Best, Magdalena, Helena & Federica

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Freesurfer February 2021