Freesurfer August 2020

freesurfer@nmr.mgh.harvard.edu

101 participants
152 discussions

mri (of an 6-year-old; 9-year-old child): recon-all error
by Wilpert, Nina- Maria 27 Aug '20

27 Aug '20

External Email - Use Caution Hello FreeSurfer Developers, We are attempting to run the command recon-all on pediatric MRI images, as described on your website: cmd="recon-all -i $Dir/*.nii.gz -s sub02_test -all" The command worked well for some of our subjects. For others (#2 3 years, 1 months; #6 6 years, 10 months; #3 9 years, 4 months), however, hard failures occurred and recon-all did not finish or we received the following error (please find the recon-all.log attached): "recon-all -s sub02_reconall exited with ERRORS at...." We are well aware that the adult Freesurfer pipeline is not recommended for children under the age of 4 years and the recently published infant Freesurfer pipeline is to be used instead. Since subject#6 and #3 and well above this age, however, we wanted to ask whether you would have any recommendations on how to trouble-shoot these issues? We have attached the recon-all.log documents in case it's of any use. 1) FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c 2) Platform: Linux 4) recon-all.log: see attached. We would very much appreciate your help! Kind regards, Nina Wilpert Nina-Maria Wilpert | medical student T +49 (0) 30 450559858 | M +49 (0) 15783851445 E nina-maria.wilpert(a)charite.de<mailto:nina-maria.wilpert@charite.de> Department of Neuropediatrics Charité, Universitätsmedizin Berlin Institute of Anatomy University of Leipzig Genetics and Development of the Cerebral Cortex Hôpital Necker-Enfants malades & IMAGINE, Paris

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Error using segmentHA_T1.sh
by Blanpain, Lou 26 Aug '20

26 Aug '20

External Email - Use Caution Hello, I attempted using segmentHA_T1.sh after running recon-all on a subject, but got the following error: “ Error using segmentSubjectT1_autoEstimateAlveusML (line 72) Side must be 'left' or 'right' “ I am using the following specs: _ platform: MacOS Catalina version 10.15.5 _ freesurfer version: 7.1.0 Could you help me with this matter? Thank you so much in advance for any input you may be able to provide regarding this! ________________________________ This e-mail message (including any attachments) is for the sole use of the intended recipient(s) and may contain confidential and privileged information. If the reader of this message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this message (including any attachments) is strictly prohibited. If you have received this message in error, please contact the sender by reply e-mail message and destroy all copies of the original message (including attachments).

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Run recon-all in MATLAB
by Camargo, Aldo 26 Aug '20

26 Aug '20

External Email - Use Caution Hi Freesurfer community, Does someone know how to run recon-all on MATLAB ? I tried the settings suggest on https://web.stanford.edu/group/vista/cgi-bin/wiki/index.php/FreeSurfer, but still is not working; Thanks a lot in advance and have a great day, Aldo

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Re: [Freesurfer] HBT segmentation missing voxels
by Iglesias Gonzalez, Juan E. 26 Aug '20

26 Aug '20

Dear Liz, Other than killing the fissure, the rest should be the same. Could you please send us un example? Cheers, /Eugenio Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com On 8/26/20, 11:30, "freesurfer-bounces(a)nmr.mgh.harvard.edu on behalf of Lizbeth Ayoub" <freesurfer-bounces(a)nmr.mgh.harvard.edu on behalf of lizbeth.ayoub(a)utoronto.ca> wrote: External Email - Use Caution Hello there, I am using Freesurfer v7.1.0 software, and I am interested in the longitudinal segmentation of the hippocampus (HBT). I am currently inspecting my output hippocampal segmentations, and couldn’t help but noticing missing voxels in the HBT mask only and not in the FS60 and CA outputs. There are voxels missing across the hippocampus, mostly body and head, when looking at the sagittal scan of the HBT output only. I am asking the following questions: 1) Why are there voxels missing in the HBT output and not in the FS60 or CA? 2) How can I fix this, as this is important for accuracy when extracting hippocampal subregion volumes? Thank you for your help, Liz _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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HBT segmentation missing voxels
by Lizbeth Ayoub 26 Aug '20

26 Aug '20

External Email - Use Caution Hello there, I am using Freesurfer v7.1.0 software, and I am interested in the longitudinal segmentation of the hippocampus (HBT). I am currently inspecting my output hippocampal segmentations, and couldn’t help but noticing missing voxels in the HBT mask only and not in the FS60 and CA outputs. There are voxels missing across the hippocampus, mostly body and head, when looking at the sagittal scan of the HBT output only. I am asking the following questions: 1) Why are there voxels missing in the HBT output and not in the FS60 or CA? 2) How can I fix this, as this is important for accuracy when extracting hippocampal subregion volumes? Thank you for your help, Liz

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Global surface area and global thickness values
by Palin, Tara 26 Aug '20

26 Aug '20

External Email - Use Caution Hello freesurfer experts, I am looking to extract the global surface and global thickness measurements and am curious if my understanding of the output on the aparc.stats (for lh and rh) are correct. When looking at these files, at the very top you will find the Pial Surface Total Area and a Mean Thickness value which I am assuming are the global measures. Below you have all of the ROIs listed (this was not changed by us or generated by us this is what comes out of freesurfer to my understanding) that includes everything EXCEPT the corpus callosum and the unknown. However, I summed all the surface areas and took and average of all the thickness measurements and they are very close to the values printed at the top of the sheet. Another observation I had made was that the total surface area measurement has a decimal and the surface area for the ROIs appears to be rounded and if they were not rounded the values would be the same. For the thickness values, the value I calculated and the one on the sheet are within the average of the standard deviation each other. If my understanding is incorrect please let me know and provide insight into how we may calculate these global measurements correctly. Thank you in advance for your time, Tara Palin ---------------------------------------------------------------------- Disclaimer: The materials in this e-mail are private and may contain Protected Information. Please note that e-mail communication is not encrypted by default. You have the right to request further emails be encrypted by notifying the sender. Your continued use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail.

3 6

Error message when using mri_glmfit-sim "ERROR: could not open .csd"
by Diógenes Bispo 26 Aug '20

26 Aug '20

External Email - Use Caution Hi Freesurfer Community, I'm using Freesurfer for the volumetric analysis of Parkinson's patients in comparison with a control group. While trying to execute it for a sample of 6 patients (3 from each group), I got one error during the mri_glmfit-sim. I did execute the mris_preproc and mri_glmfit before it. These are all the steps: First created the FSGD and contrast folders. I did copy the fsaverage to the local folder. All the comands were executed under the local folder within the structure: drwxr-xr-x 2 vinicius vinicius 4096 ago 3 09:53 Contrasts drwxrwxrwx 10 vinicius vinicius 4096 jun 15 10:08 DPV1_ACM1604 drwxrwxrwx 10 vinicius vinicius 4096 jun 14 22:26 DPV1_APA1311 drwxrwxrwx 10 vinicius vinicius 4096 jun 14 22:28 DPV1_CEM1702 -rw-r--r-- 1 vinicius vinicius 210 ago 3 10:12 example.fsgd drwxrwxrwx 8 vinicius vinicius 4096 nov 13 2015 fsaverage drwxr-xr-x 2 vinicius vinicius 4096 ago 3 10:14 FSGD drwxrwxrwx 10 vinicius vinicius 4096 jun 14 22:31 GCV1_FCB0701 drwxrwxrwx 10 vinicius vinicius 4096 jun 14 22:34 GCV1_JCC2509 drwxrwxrwx 10 vinicius vinicius 4096 jun 14 22:36 GCV1_JCC2902 FSGD file used was the example.fsgd and its contents are: GroupDescriptorFile 1 Title example Class CONTROLE Class PK Input GCV1_FCB0701 CONTROLE Input GCV1_JCC2509 CONTROLE Input GCV1_JCC2902 CONTROLE Input DPV1_ACM1604 PK Input DPV1_APA1311 PK Input DPV1_CEM1702 PK Created the Contrasts files CONTROLE-PK.mtx, and it's contents: 1 -1 PK-CONTROLE.mtx, and it's contents: -1 1 Used the local folder as SUBJECTS_DIR: export SUBJECTS_DIR=$('pwd') export LC_NUMERIC="en_US.UTF-8" Started with the mris_preproc: mris_preproc --fsgd /home/vinicius/fsteste/example.fsgd --cache-in volume.fwhm10.fsaverage --target fsaverage --hemi lh --out lh.volume.example.10.mgh mris_preproc --fsgd /home/vinicius/fsteste/example.fsgd --cache-in volume.fwhm10.fsaverage --target fsaverage --hemi lh --out rh.volume.example.10.mgh mris_preproc --fsgd /home/vinicius/fsteste/example.fsgd --cache-in thickness.fwhm10.fsaverage --target fsaverage --hemi lh --out lh.thickness.example.10.mgh mris_preproc --fsgd /home/vinicius/fsteste/example.fsgd --cache-in thickness.fwhm10.fsaverage --target fsaverage --hemi rh --out rh.thickness.example.10.mgh All the outputs were attached in the file mris_preproc.zip After that I did execute the mri_glmfit: mri_glmfit --y lh.volume.example.10.mgh --fsgd /home/vinicius/fsteste/example.fsgd --C /home/vinicius/fsteste/Contrasts/CONTROLE-PK.mtx --C /home/vinicius/fsteste/Contrasts/PK-CONTROLE.mtx --surf fsaverage lh --cortex --glmdir lh.volume.example.10.glmd mri_glmfit --y rh.volume.example.10.mgh --fsgd /home/vinicius/fsteste/example.fsgd --C /home/vinicius/fsteste/Contrasts/CONTROLE-PK.mtx --C /home/vinicius/fsteste/Contrasts/PK-CONTROLE.mtx --surf fsaverage rh --cortex --glmdir rh.volume.example.10.glmd mri_glmfit --y lh.thickness.example.10.mgh --fsgd /home/vinicius/fsteste/example.fsgd --C /home/vinicius/fsteste/Contrasts/CONTROLE-PK.mtx --C /home/vinicius/fsteste/Contrasts/PK-CONTROLE.mtx --surf fsaverage lh --cortex --glmdir lh.thickness.example.10.glmd mri_glmfit --y rh.thickness.example.10.mgh --fsgd /home/vinicius/fsteste/example.fsgd --C /home/vinicius/fsteste/Contrasts/CONTROLE-PK.mtx --C /home/vinicius/fsteste/Contrasts/PK-CONTROLE.mtx --surf fsaverage rh --cortex --glmdir rh.thickness.example.10.glmd All the outputs were attached in the file mris_preproc.zip When I try to execute the mri_glmfit-sim with the command: mri_glmfit-sim --glmdir lh.volume.example.10.glmd --cache 1.3 pos --cwp 0.05 --2spaces I get the following error: ERROR: could not open lh.volume.example.10.glmd/csd/all.cache.th13.pos-CONTROLE-PK.csd The folder lh.volume.example.10.glmd/csd was not created. All subjects were processed using version 7 without qcache and then executed the qcache separately later on. Attached the entire output of the command: output_lh.volume.example.10.glmd.txt Also attached the summary of the lh.volume.example.10.glmd cache.th13.pos.sig.cluster.summary System: Ubuntu LTS 18.04. Please, help me to fix this error or help me to figure out what I'm doing wrong. Thank you! Diógenes Bispo diogenesdiego(a)gmail.com

3 7

WM & GM mean thickness
by vittal korann 26 Aug '20

26 Aug '20

External Email - Use Caution Dear FreeSurfer experts I'm trying to get global mean thicknesses of white matter and gray matter separately. But *stats* folder in the *subjects *list does not mention explicitly. Is there a way to get these two thicknesses? Any assistance would be appreciated with deep respect. With regards Korann

2 1

use of ANTs Denoising in FS 7.1
by Alexopoulos, Dimitrios 26 Aug '20

26 Aug '20

External Email - Use Caution Hi all, In previous datasets, and prior to FS 7, we independently ran ANTs denosing on the input T1s prior to running recon-all, However, FS 7.1 now appears to use the denosing utility in parts of the pipeline. "ANTS denoise is used when creating the orig surface (but not thefinal surfaces)" Does this mean the denoised image is only used in the segmentation part of the pipeline (to generated the aseg.mgz) and does not propagate through to final surfaces? Why not use denoised T1 through the surface-generation phase of the pipeline. Can you provide some further clarification. Thx. 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.

3 5

missing one tract but differently for a few subjects
by Zeng, Qi 25 Aug '20

25 Aug '20

External Email - Use Caution Hi, When I examined the 18 tracts of /dpath results, a few subjects were found missing one tract but differently, for example, fmajor were missing for one subject and the other one was missing lh.slfp and rh.slfp. I was thinking could it be that AP-PA was flipped. Attached screenshots of dtifit_FA.nii, aparc+seg_mask.nii, and bvec. Can you provide some information about the flip so that I can examine it for the rest of the subjects? Best, Qi --

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Freesurfer August 2020