Freesurfer

freesurfer@nmr.mgh.harvard.edu

18 participants
30131 discussions

Different results on same MRI in different space ?
by Funk, Quentin 11 Feb '21

11 Feb '21

External Email - Use Caution Freesurfer experts, I have two MRIs for a patient separated by 5 years. I would like to look at progression of atrophy. These MRIs are different, however, firstly in terms of resolution (new one is 1x1x1, old one is 1.05x1.05x1.2), and secondly just in terms of general contrast, as they are different protocols from different scanners. First I ran Freesurfer 6.0.0 on both MRIs; but the results I obtained didn't make much sense -- when I compared to a group of controls, the thickness values were much lower in the old MRI than in the new one. This could, of course, be due to variance in contrast / type of scanner, etc. Reviewing the surfaces, in both cases (old and new), all surfaces looked very good with no major errors. I wanted to see how well the surfaces lined up over time -- so I wanted them in the same space. To get this, I co-registered the new MRI to the old one (via SPM), and re-ran recon-all on it. Now, when I compare to a group of controls, the new MRI has much more expected results -- e.g. lower thickness than the old one. Again, surfaces looked very good. All that changed is the space the MRI was in when I fed it into FS -- some slight variance from voxel resolutions aside, this gave very different results. I looked at the lh.aparc.stats files and computed some percent differences and was pretty surprised by what I saw. For example, GrayVol values were different by 20% in the precentral, thickaverage was off by 17% in the precuneus. obviously I made an error somewhere that caused this type of variance but I can't find it -- is there any advice for comparing this type of longitudinal data ? thank you for any help you can provide! Quentin Funk, PhD Houston Methodist Research Institute 713-363-9003<tel:713-363-9003> Houston Methodist. Leading Medicine. Houston Methodist is ranked by U.S. News & World Report as the No. 1 hospital in Texas for patient care and safety and one of the top 20 hospitals in the nation. In addition, we are nationally ranked in 11 specialties, the most in the state, and have been national leaders throughout the COVID-19 pandemic in research, offering innovative treatments and surpassing CDC safety standards. For more than 100 years, Houston Methodist has provided the best — and safest — clinical care, advanced technology and patient experience. That is our promise of leading medicine. houstonmethodist.org twitter.com/MethodistHosp facebook.com/HoustonMethodist ***CONFIDENTIALITY NOTICE*** This e-mail is the property of Houston Methodist and/or its relevant affiliates and may contain restricted and privileged material for the sole use of the intended recipient(s). Any review, use, distribution or disclosure by others is strictly prohibited. If you are not the intended recipient (or authorized to receive for the recipient), please contact the sender and delete all copies of the message. Thank you.

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Installing anither Freesurfer version - lincese not working
by Fernanda Hansen P. de Moraes 11 Feb '21

11 Feb '21

External Email - Use Caution Dear Freesurfer experts, I installed another Freesurfer version on my computer and used the same license of the version installed before. But, it is not working. How should I proceed? Best regards, Fernanda Hansen P. de Moraes fernandahmoraes(a)gmail.com Doutoranda em Ciências Médicas | Instituto D'Or de Pesquisa e Ensino (IDOR), Rio de Janeiro, Brazil

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Compute geometric mean of 32 b1000 images (DTI)
by Mateus Aranha 11 Feb '21

11 Feb '21

External Email - Use Caution Dear all, I have 32 directions DTI images and I need to compute DWI and ADC maps from these images. As far as I know the DWI is obtained by calculating the geometric mean of the 32 b1000 images. Can it be done with mri_concat --gmean Ng? Many thanks, Mateus

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For multiple comparisons
by Kim, Gwang-Won 11 Feb '21

11 Feb '21

Hi there, First, I ran "mri_glmfit" using a mask (subcortical regions) as follows: mri_glmfit --glmdir g1v1.wls --y ces.nii.gz --wis cesvar.nii.gz --fsgd g1v1.fsgd --C age.mtx --mask brain.mni305.2mm.nii.gz --fwhm 5. Second, I'm going to process "mri_glmfit-sim" to perform a cluster-wise correction for multiple comparisons. Which I select the comment? 1) mri_glmfit-sim -glmdir g1v1.wis -3spaces -grf 2 abs 2) mri_glmfit-sim -glmdir g1v1.wis -perm 1000 2.0 abs -cwp 0.05 -3spaces -bg 16 Especially, I use the mask the subcortical regions, not cortical regions. Should I remove “-3spaces” in the commend or what do I do instead of “-3spaces”? Thank you, Gwang-Won

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Recon error
by Bohorquez Montoya, Luisa 11 Feb '21

11 Feb '21

External Email - Use Caution Hello Freesurfer I have been trying to run this subject 3 times (with different walltime) and I am having the same error. Would you mind please to explain me what I am doing wrong? Thank you subject="$1" echo $subject cd /scratch/global/lbohorquez/Freesurfer/"$subject" export SUBJECTS_DIR=/scratch/global/lbohorquez/Freesurfer/"$subject" ANATDIR=/scratch/global/lbohorquez/Freesurfer/ OPENMP=12 export OMP_NUM_THREADS=12 recon-all \ -autorecon2 -autorecon3 -subject "$subject" \ -no-isrunning -parallel -openmp 12 \ ####SUMA-ize with AFNI echo "Before Suma" @SUMA_Make_Spec_FS -NIFTI \ -fspath ${SUBJECTS_DIR}/"$subject" \ -sid "$subject" echo "After Suma" ######## registration TO MNI cd ${SUBJECTS_DIR}/"$subject"/SUMA/ @SSwarper -input "$subject"_SurfVol.nii -base MNI152_2009_template_SSW.nii.gz -subid ssWarp Luisa Bohorquez, PhD. Department of Psychiatry, Medical College of Wisconsin.

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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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Freesurfer