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30132 discussions

Volume correction with Intracranial volume
by Steve Petersen 10 Jan '20

10 Jan '20

External Email - Use Caution Dear Freesurfer experts, I would like to perform external analysis with the hippocampus, parahipocampus and entorhinal volume. As I understand its the hipocampo volume should be corrected using the subject´s intracranial volume. 1. How do you recommend correcting the volumes (hippocampus, parahipocampus and entorhinal cortex) with the intracranial volume? Maybe correcting the volume by scaling with the EstimatedTotalIntraCranialVol? 2. Is necessary to correct the cortical thickness measurements with the intracranial volume? Thanks for your help. Best regards,

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Lesion Correction
by Horn, Mitchell Jacob 10 Jan '20

10 Jan '20

Hi Freesurfer Team, I have a couple cases with large hemispheric ICH that have caused my recon to hit the default wall-time of 96 hours. It seems to get hung up on the correcting topology defects step for the affected hemisphere. My goal is to have the recon at least finish so I can analyze the unaffected hemisphere. I have tried WM-edits, and just recently tried generously covering the ICH in the aseg.presurf with the WM-hypointensity label 77. I then submitted the recon to start just after the aseg.presurf generation with the following tags, < recon-all -autorecon2-cp -autorecon3 -subjid $subject >. However, when it gets to the fix topology point for the affected hemisphere, it hangs at this point with a huge defect as shown below: reading brain volume from brain... reading wm segmentation from wm... Reading original properties of orig.nofix Reading vertex positions of inflated.nofix Computing Initial Surface Statistics -face loglikelihood: -9.2324 (-4.6162) -vertex loglikelihood: -6.5360 (-3.2680) -normal dot loglikelihood: -3.5251 (-3.5251) -quad curv loglikelihood: -6.0339 (-3.0169) Total Loglikelihood : -25.3274 CORRECTING DEFECT 0 (vertices=26285, convex hull=5359, v0=0) Is there something I can do to at least skip the correction of the affected hemisphere? Thanks in advance, Mitch

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Freesurfer 7T MPRAGE
by Manoj Saranathan 10 Jan '20

10 Jan '20

External Email - Use Caution Hi, I am trying to process 7T MPRAGE data (not MP2RAGE) using recon-all. In previous threads, a few people have suggested using SPM to correct for bias first and then running recon-all. Alternatively I saw a thread which suggests modifying the mri_nu_correct command https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg61913.html Can I edit the recon-all to run this alternative command and simply run recon-all? The threads are all really old and SPM is now SPM12 which integrates things. Is this modified bias correction inside FS as good as SPM ? I am mainly interested in thalamic segmentation. Are there others with the same issue? Thanks manoj Manoj Saranathan Associate Professor, Dept. of Medical Imaging University of Arizona Ph: 520-626-6531

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pcc.mgh files from mri_glmfit using --pvr
by Emilie Reas 10 Jan '20

10 Jan '20

External Email - Use Caution I am running mri_glmfit using the --pvr option and do not get a pcc.mgh file with the output. I found an old thread from 2017 in which Douglas Greve explained that "mri_glmfit will not generate a pcc file with --pvr. I think I just did not get around to adding support for this." Have there been any updates to fix this? Is there a workaround to get pcc files using --pvr? -- Emilie Reas, PhD Postdoctoral Fellow, UC San Diego ereas(a)ucsd.edu

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Anterior parts of Temporal Lobe missing
by Meike Hettwer 10 Jan '20

10 Jan '20

External Email - Use Caution Hi everyone, I am currently working on cortical thickness analyses using freesurfer v. 6.0.1. (on Debian /Linux 7). All of my data sets show a segmentation error in the anterior protions of the temporal lobe (mostly STG and almost always bilateral). I tried adding control points as well as editing wm.mgz manually. It does not seem to help much, though. After running "recon-all -autorecon2-cp -autorecon3 subjid .." without errors, the images look just the same (just with the green control points lighting up). I saw that other users encountered similar problems but did not find a solution in the archives. Does anyone have an idea how to fix this? The intensity values are around 73 for white matter and 46 for grey matter. Thanks a lot in advance, Meike Hettwer

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Fixing wm/gm in brain with a cyst
by Laurel Quinlan 09 Jan '20

09 Jan '20

External Email - Use Caution Hi FS Support, I am working on manual edits to a brain with a suspected cyst. Attached is an axial view of the original recon. As you can see, there appears to be wm missing from the segmentation right next to the cyst. I am wondering how I should go about fixing the segmentation with this brain. Should I fill in the missing white matter next to the ventricular hole, and avoid adding anything to the hole itself? Or is there another step I should take? Thanks! Laurel Quinlan Research Specialist Center for Healthy Minds University of Wisconsin-Madison

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Re: [Freesurfer] Error
by fsbuild 09 Jan '20

09 Jan '20

External Email - Use Caution Hello Kirill, Is the shared folder where the “ln -s” command is running to create a soft link on a disk that is formatted to have a Windows file system, e.g., NTFS?   My understanding is that Linux/Unix style soft linking via the “ln” command does not work on such a windows file system.  Freesurfer scripts assume the file system supports standard Unix/Linux soft links via the ln command, e.g., where the disk partition or volume it runs on is formatted as ext3 or ext4. You can install software in Windows to *read* a linux file system.  The link below talks about 2 software applications for windows -  one can read linux file systems, and the other can read both linux and Mac file systems. https://www.howtogeek.com/112888/3-ways-to-access-your-linux-partitions-fro… - R. A Windows NTFS file system does not support Unix soft links On Jan 9, 2020, at 08:58, Kirill Elin <ekirling(a)gmail.com> wrote:       External Email - Use Caution        Dear FreeSurfer Developers,I am trying to run the script and the recon-all command and gettingExited with errors output.1. FreeSurfer Version freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c2. Platform, VM Ware Workstation 15, host OS: Windows 10, Guest:Ubuntu ubuntu-18.04.3-LTS, 64 Bit, 2 GB RAM3. See the log file and the screenshot.In the script I have not found any other errors so I am not even sure,what I should be looking for.If it plays a role, my MRI folder, where original T1s are as well asthe output folder are in the shared folder (shared between the hostwindows OS and the virtual machine).I would be grateful if you could help me out with this.Thank you in advance.Sincerely yours,Kirill<Finish_Errors.PNG><recon-all.log>_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] Projection on fsaverage5
by Marina Fernández 09 Jan '20

09 Jan '20

External Email - Use Caution Hi Doug, Thank you for your advice. I checked the results using ico 5 and fsaverage5 and it seems to have exactly the same values, but we are going to use --trgsubject fsaverage5, as you told me. On the other hand if we use EPI that it is coregistered to the T1 of Freesurfer there is no problem with the projection on fsaverage5. Thank you very much! Cheers, Marina

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RB_all_2020-01-02.gca and RB_all_withskull_2020_01_02.gca public permissions
by Kostakis Gkiatis 08 Jan '20

08 Jan '20

External Email - Use Caution Dear Freesurfer experts, I am trying to compile freesurfer from source. It is nicely performed expect the "git annex get ." command which fails in these two files, RB_all_2020-01-02.gca and RB_all_withskull_2020_01_02.gca. I searched github's annex branch but no sign of the files. Do I have, as public, the right permissions to download them? Can I find these two files somewhere else? Thank you in advance. Yours sincerely, Kostakis -- Electrical and Computer Engineer Phd Candidate in Brain Imaging Medical Image Processing, Algorithms and Applications National Technical University of Athens 9,Iroon Polytechneiou str., 157 73 Zografou Campus, Athens, GREECE phone:+30 210 772 3577

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Projection on fsaverage5
by Marina Fernández 08 Jan '20

08 Jan '20

External Email - Use Caution Hi Bruce, Thanks for the quick response. I found that the problem was the input. If I use the EPI that it is coregistered to the T1 of Freesurfer instead of the EPI that it is also normalized to the MNI space, it works and I can project the surface (that I created with the command that I sent you) on fsaverage 5. Could you confirm that the command has no errors? mri_vol2surf --mov EPI.nii --reg register.dat --hemi [l/r]h --projfrac 0.5 --interp trilinear --trgsubject ico --icoorder 5 --o EPI_surface.mgh Best wishes, Marina

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