Freesurfer

freesurfer@nmr.mgh.harvard.edu

18 participants
30131 discussions

Convert image in native coordinate space
by Haiyun Chen 08 Nov '22

08 Nov '22

External Email - Use Caution Hello FreeSurfer Experts, Could you help to tell how can we convert the file lh.pial.native to Nifti file or Dicom file? The file lh.pial.native is generated by FreeSurfer as mentioned in your website: https://secure-web.cisco.com/1OqLwwMukRA3gBsB4xIyWu7jYzQnxoAsxTmCFH4BX5vUNN… <https://secure-web.cisco.com/1ADHgS0v8L4KAY_-4Q1wqkSQ0S5tB-9JDHvuOQr01nK4OE…> Thank you in advance for your help! Best regards Haiyun

2 2

design is ill-conditioned
by Loeffler, Martin 08 Nov '22

08 Nov '22

External Email - Use Caution Dear experts, I’m running into an error when running selxavg3. It says the design is ill-conditioned. I’m a bit stuck, because the same pipeline works in most subjects, but not all. Also, if I exchange the functional scan (f.nii.gz) with a scan from a working session of the same subject (same number of volumes etc.) I don’t get any errors. I’m grateful for any advice that helps to track down the mistake I’m doing. Here the content of the selxavg3.log file: cd /home/hector/SENS_MAPPING_BLOCK/sessions /opt/software/freesurfer/fsfast/bin/selxavg3-sessbc -s HEC_035_1 -analysis MPBDandefs_orig_lhrh_revd11.5_sm2.lh -no-preproc -fwhm -force Found 42449/139130 (30.5) voxels in mask Creating Design Matrix ... creation time = 0.004 sec DoMCFit = 1 ntptot = 500, nX = 33, DOF = 467 XCond = 2.63784e+16 (normalized) ERROR: design is ill-conditioned Before the error it gives a warning that the design matrix is singular or badly scaled: [Warning: Matrix is close to singular or badly scaled. Results may be inaccurate. RCOND = 1.271035e-17.] [> In fast_selxavg3bc (line 318)] norm(inv(XtX),2) = [14601308845709730.0] Saving X matrix to /home/hector/SENS_MAPPING_BLOCK/sessions/HEC_035_1/bold/MPBDandefs_orig_lhrh_revd11.5_sm2.lh/Xtmp.mat XCond = 2.63784e+16 (normalized) ERROR: design is ill-conditioned >> ------------------------------------------ ERROR: fast_selxavg3bc() failed\n Many thanks in advance, Martin

2 1

Cutting an occipital patch
by Noam Khayat 08 Nov '22

08 Nov '22

External Email - Use Caution Hello, I need to cut the occipital pole in order to make a retinotopy analysis. I read that tksurfer no more exists, and with freeview I only succeed in cutting the plane but I'm having trouble with separating it into a patch with the occipital part only. Do you know if there is a way to do this? Thanks! Noam

2 7

Question about color look up table
by Yoshito Saito 08 Nov '22

08 Nov '22

External Email - Use Caution Hello. I would like to ask a question about the color look-up table. I want to change the opacity of color on a brain atlas in Freeview. I changed the number in a column of opacity in the Color Lookup Table file by following the instructions on this website ( https://secure-web.cisco.com/1DQQao3VQ454IQKL-p8fj3rK0Jciinx1EwjIuNuRgfloa5…) but I could not change the opacity at all. I am using a bit old version of FreeSurfer (ver 6.0) on the HPC of my university, but is this the reason I couldn't change it? I am looking forward to hearing from you. Sincerely, Yoshito -- Yoshito Saito MBBS Master's candidate (Master of Philosophy - Medicine) Melbourne Neuropsychiatry Centre The University of Melbourne

2 1

intensity statistics in aseg.stats
by Zeng, Qi 08 Nov '22

08 Nov '22

External Email - Use Caution Hi Freesurfer scholars, The output of recon-all "aseg.stats" file contains information on volume and intensity statistics of each segmentation of subcortical brain regions. May I ask what is this intensity measurement (e.g. intensity mean)? How is it different from volume? What characteristics of the brain did it try to explain? Thank you! Best, QZ

2 1

dcmunpack
by Jang, Woo Ju Albert W.,PhD 08 Nov '22

08 Nov '22

Hi, I need to unpack dcm files to my local workstation via dcmunpack command. Is it possible to install this command on my local workstation? Best, Albert

2 1

change in mask size
by priya padma 08 Nov '22

08 Nov '22

External Email - Use Caution Dear Team, I tried using freesurfer for skull stripping and I got results all of size 256X256X256 but the original data size is different, it's 512X512X537. Is there any way to bring back the original size in freesurfer? Any help would be appreciated. Thank you -- Best Regards Padma Priya *AI Developer * *PhenoMx, Inc.* *priya(a)phenomx.ai <priya(a)phenomx.ai> | (+82)10-5405-2685*

3 2

Question regarding General Linear Model analysis with Freesurfer
by Lyna Mariam El Haffaf 08 Nov '22

08 Nov '22

External Email - Use Caution Hi! I hope you are doing well! I am working on a paper where we used Freesurfer for whole brain analysis in intergroup comparison (g2v1). The objective of the analysis is to see if there is an association between neuropsychiatric symptoms and brain regions at different stages of Alzheimer's disease (Alzheimer, Mild cognitive impairment and cognitively normal participants). For this objective, a whole-brain analysis was performed using general linear model (GLM) analysis with FreeSurfer mri_glmfit for each neuropsychiatric symptoms of interest to assess their effect on brain’s cortical volume, thickness and area, between the groups (AD vs MCI, CN vs MCI, CN vs AD). We performed a Monte-Carlo correction on the results obtained. I was wondering if it was possible to add another correction for multiple group comparison in addition to the Monte-Carlo correction? Also, is it possible to add covariates by creating additional models using the GLM analysis with Freesurfer mri_glmfit? Thank you in advance! Lyna El Haffaf Graduate student in neuropsychology Université de Montréal

2 1

Re: [Freesurfer] Segmentation Fault (Ventura)
by fsbuild 07 Nov '22

07 Nov '22

External Email - Use Caution Hello Joann, If I read correctly, you are doing a remote mount of a shared network drive to your Mac to store/read/write the subject files but running the recon-all using your Mac processors. You might want to check the directory for the last subject processed to see if there are log files with any more info.  A segmentation fault can happen for various reasons, but we might be able to tell something if you can get a hold of the core dump file. There could be differences w.r.t  how Ventura maintains a connection to and interacts with a remote file system compared to Monterey, e.g., timeouts, authentication, file caching, etc .  If recon-all was proceeding normally and then no longer could see or access the remote file system when it needed to read or write a file, then the recon-all would fail.  But I would expect to see some message w.r.t file not found, permission denied and not just a segfault message. We have have not done any testing with MacOS Ventura and we don’t generally test on MacOS using remotely mounted file systems.  Many Mac users I know always stay one operating system release behind the latest version of MacOS.  They are only now upgrading from BigSur to Monterey since Ventura was officially released last month.   If I have test the latest release I try to wait until the first .1 release is out as the initial .0 releases are often the most buggy (for Ventura that would mean waiting for 13.1). - R. On Nov 7, 2022, at 17:27, Joann Stewart <stewart.joann3(a)yahoo.com> wrote:        External Email - Use Caution        Hello, I am attempting to analyze some structural morphometry data. I am having issues with the recon-all command that I am using. I am attempting to run this command on a shared network folder through my institution. Here is the exact command I am using : recon-all -subject 1306_A -i 1306/T1w/T1w_MPR.nii.gz -T2 1306/T2w/T2w_SPC.nii.gz -T2pial -all -qcache   On the server, when I run this command, it continues until I get to the segmentation portion. I have the full output of this command attached to the email in a word document titled “Recon-all output on server”. Attached I also have a copy of the recon-all.log file. There is another member in my lab who was able to use this command successfully with the same files and exact same code. He was using the same server that I was on, and we have exactly the same permissions on the server. The only difference is that I have updated my mac to Ventura and he has not yet updated his mac (he is using macOS Monterey 12.6).  We tried moving my files onto my desktop to see if the recon-all worked there as compared to the server. I simply moved the T1w & T2w NIfTI files onto my desktop from the server. When I run recon all sourcing from the NIfTI files on my desktop rather than the server, it works fine without error.  Therefore, we are wondering if it is an issue with the new Ventura update in conjunction with shared network folders. Do you have any suggestions or ideas based on the information I have provided? FreeSurfer version: freesurfer-darwin-macOS-7.3.2-20220804-6354275Platform: MacOS Ventura 13.0 Let me know if there is any more information that you need.  Thank you!<Recon-all output on server.docx><recon-all.log>_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

1 0

Segmentation Fault (Ventura)
by Joann Stewart 07 Nov '22

07 Nov '22

External Email - Use Caution Hello, I am attempting to analyze some structural morphometry data. I am having issues with the recon-all command that I am using. I am attempting to run this command on a shared network folder through my institution. Here is the exact command I am using : recon-all -subject 1306_A -i 1306/T1w/T1w_MPR.nii.gz -T2 1306/T2w/T2w_SPC.nii.gz -T2pial -all -qcache On the server, when I run this command, it continues until I get to the segmentation portion. I have the full output of this command attached to the email in a word document titled “Recon-all output on server”. Attached I also have a copy of the recon-all.log file. There is another member in my lab who was able to use this command successfully with the same files and exact same code. He was using the same server that I was on, and we have exactly the same permissions on the server. The only difference is that I have updated my mac to Ventura and he has not yet updated his mac (he is using macOS Monterey 12.6). We tried moving my files onto my desktop to see if the recon-all worked there as compared to the server. I simply moved the T1w & T2w NIfTI files onto my desktop from the server. When I run recon all sourcing from the NIfTI files on my desktop rather than the server, it works fine without error. Therefore, we are wondering if it is an issue with the new Ventura update in conjunction with shared network folders. Do you have any suggestions or ideas based on the information I have provided? - FreeSurfer version: freesurfer-darwin-macOS-7.3.2-20220804-6354275 - Platform: MacOS Ventura 13.0 Let me know if there is any more information that you need. Thank you!

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