Freesurfer

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Re: [Freesurfer] if: Expression Syntax - preproc-sess
by Douglas N. Greve 22 Mar '24

22 Mar '24

Hi Stefano, I think I found and fixed the problem. Can you try these? On 3/19/2024 7:30 AM, Stefano Delli Pizzi wrote: > > External Email - Use Caution > > Hi Doug, > > The raw functional file is firstly passed with motion correction > (i.e., mc-sess -s ID -fsd rest -per-run) and AROMA filtering. > Next, I have renamed the ICA filtered file as f.nii.gz. > Then, I run: > > preproc-sess -s ${1} -surface fsaverage lhrh -nomc -fwhm 0 -mni305 > -fsd rest -per-run -sliceorder even -force > > There are issues with labels since excluding motion correction doesn't > produce key files necessary for concatenating the files. > The preprocessing script is searching for the fmcpr.nii.gz file, which > cannot be found because it is not created using the -nomc option. > > When I duplicate and rename the file f.nii.gz as fmcpr.nii.gz and > rerun preproc, the operation is done and the > fmcpr.odd.sm0.fsaverage.lh is created. > > However, when I run the next steps (fcseed-sess -s ID -cfg wm.config > -overwrite), a second error occurs (reported below) because the script > searches for fmcpr, which cannot be produced since I used -mc. > > ERROR: could not determine file for > /Volumes/mnu/MRI/PPMI/NIFTI/FreeSurfer/rs-fMRI_AROMA/ID/rest/001/fmcpr > This error seems to be related to the script searching for the fmcpr > file, which isn't available due to the use of -mc. > > Thank you. > > Best regards, > > > Stefano > > > > >> Il giorno 18 mar 2024, alle ore 17:16, Stefano Delli Pizzi >> <sdellipizzi(a)gmail.com> ha scritto: >> >> Hi Doug have you any news >> Thank you very much! >> Stefano >> >>> Il giorno 12 mar 2024, alle ore 10:26, Stefano Delli Pizzi >>> <sdellipizzi(a)gmail.com> ha scritto: >>> >>> Thank you. >>> I’m attaching the file. >>> Stefano >>> <preproc-sess> >>> >>>> Il giorno 11 mar 2024, alle ore 22:20, Douglas N. Greve >>>> <dgreve(a)mgh.harvard.edu> ha scritto: >>>> >>>> can you send me this file >>>> /Applications/freesurfer/7.4.1/fsfast/bin/preproc-sess >>>> >>>> >>>> On 3/11/2024 3:58 AM, Stefano Delli Pizzi wrote: >>>>> >>>>> External Email - Use Caution >>>>> >>>>> It seems to me that I've done what you suggest. Attached is a new >>>>> outputs. >>>>> Thanks >>>>> Stefano >>>>> >>>>>> Il giorno 10 mar 2024, alle ore 23:44, Douglas N. Greve >>>>>> <dgreve(a)mgh.harvard.edu> ha scritto: >>>>>> >>>>>> Are you sure that you are using the new version that I gave you? >>>>>> It looks like the previous version. Also, it does not look like >>>>>> the entire terminal output. >>>>>> >>>>>> On 3/8/2024 12:11 PM, Stefano Delli Pizzi wrote: >>>>>>> >>>>>>> External Email - Use Caution >>>>>>> >>>>>>> The entire terminal output is attached. >>>>>>> Thanks! >>>>>>> >>>>>>>> Il giorno 8 mar 2024, alle ore 15:56, Douglas N. Greve >>>>>>>> <dgreve(a)mgh.harvard.edu> ha scritto: >>>>>>>> >>>>>>>> entire terminal output >>>>>>> >>>>>> >>>>>> _______________________________________________ >>>>>> Freesurfer mailing list >>>>>> Freesurfer(a)nmr.mgh.harvard.edu >>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>> 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 >>>>>> https://www.massgeneralbrigham.org/complianceline >>>>>> <https://www.massgeneralbrigham.org/complianceline> . >>>>> >>>> >>>> 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 >>>> https://www.massgeneralbrigham.org/complianceline >>>> <https://secure-web.cisco.com/1jYq_7i1WV2KuJNwpF_8LuUmEt1uXm4GShRtNXC1xe4Y_B…> >>>> . >>>> >>> >

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Re: [Freesurfer] Mac OS Monterrey and XQuartz 2.8.2
by fsbuild 21 Mar '24

21 Mar '24

External Email - Use Caution I would try downloading an installing the latest version of Xquartz which is 2.8.5 from,https://secure-web.cisco.com/1QbY1_LKpOs8rxg9YmC2vjno1Z4v2i9V4XhLfDJzw… Works fine with Monterey (at least on an Intel Mac). - R. On Mar 21, 2024, at 19:05, Hugo Sandoval <guayosandoval(a)gmail.com> wrote:        External Email - Use Caution        Hi, i am trying to install freesurfer using Mac OS Monterrey and XQuartz 2.8.2.  I get an error message.  Is it not compatible?_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Mac OS Monterrey and XQuartz 2.8.2
by Hugo Sandoval 21 Mar '24

21 Mar '24

External Email - Use Caution Hi, i am trying to install freesurfer using Mac OS Monterrey and XQuartz 2.8.2. I get an error message. Is it not compatible?

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What do the stats files tell us?
by Vivek Kandasamy 21 Mar '24

21 Mar '24

External Email - Use Caution Hello, So I ran FreeSurfer to get numeric data from MRI images and got these files under the stats page. [image: Screenshot 2024-03-18 144107.png] Do you know what each file tells us about our MRI images such as the lh.aparc.DKTatlas.mapped, lh.BA_exvivo.stats, lh.BA_exvivo.thresh, lh.curv, lh.w-g.pct, and wmparc.DKTatlas.mapped files? Thanks, Vivek Kandasamy

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Bug reporting - longmc: case-sensitive issue in variable
by Boscutti, Andrea 20 Mar '24

20 Mar '24

External Email - Use Caution Hello FreeSurfer Developers, When attempting to run "recon-all -long" in subjects with multiple T1 inputs, I get the following error when "longmc" is run: concatLtas: Undefined variable. if: Expression Syntax. Command exited with non-zero status 1 For the entire log, see attached "longmc_error.log". The following change at line 188 of "freesurfer/bin/longmc" fixes it (case-sensitive issue in "$concatLtas"): set ud = `UpdateNeeded $origvol $CrossList $concatLtas --> set ud = `UpdateNeeded $origvol $CrossList $ConcatLtas` Best, Andrea

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Re: [Freesurfer] Bug reporting - longmc: case-sensitive issue in variable
by fsbuild 19 Mar '24

19 Mar '24

External Email - Use Caution  On Ubuntu linux the default shell may still be “dash” and not the “bash” shell.  Dash cannot parse all bash scripting, so type “bash” or try setting “bash” to be your default shell and then run commands. - R. On Mar 19, 2024, at 22:17, Boscutti, Andrea <Andrea.Boscutti(a)uth.tmc.edu> wrote:        External Email - Use Caution        Hello FreeSurfer Developers,When attempting to run "recon-all -long" in subjects with multiple T1 inputs, I get the following error when "longmc" is run:concatLtas: Undefined variable.if: Expression Syntax.Command exited with non-zero status 1For the entire log, see attached "longmc_error.log".The following change at line 188 of "freesurfer/bin/longmc" fixes it (case-sensitive issue in "$concatLtas"):set ud = `UpdateNeeded $origvol $CrossList $concatLtas  -->  set ud = `UpdateNeeded $origvol $CrossList $ConcatLtas`Best,Andrea<longmc_error.log>_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Measure statistics from manually segmented cortical GM
by K Eswar 19 Mar '24

19 Mar '24

External Email - Use Caution Dear Freesurfer Team, My name is K Eswar, and I am reaching out to seek assistance regarding a project I am currently working on. I have manually segmented the cortical gray matter of a fetal brain MRI (nii.gz and stl formats) and now need to perform various analyses such as measuring curvature, volume, area, and thickness. As I am relatively new to using FreeSurfer, I am seeking guidance on how to effectively utilize the software for these analyses. Could you please provide me with some guidance or resources on how to proceed with this task using FreeSurfer? Any assistance or advice you could offer would be greatly appreciated. Thank you very much for your time and assistance. I look forward to hearing back from you soon. Kind regards K Eswar

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Issues with accuracy of pial and white matter surface reconstruction in infant_recon_all command
by Tsigaras, Thanos 19 Mar '24

19 Mar '24

External Email - Use Caution Dear infantFS-team, We are a team of PhD students, who recently decided to use infantFS for the segmentation and surface extraction on our data. We used the infant_recon_all command for preprocessing T1w sMRI scans from the Baby Connectome Project dataset. The pipeline runs without any errors, but we encountered noticeable inaccuracies in the reconstructed surfaces, especially concerning the pial surface. The white matter surface reconstruction was mostly accurate (with some exceptions), but in some cases even the segmentation fails as well, particularly in very young subjects. Even when the segmentation is accurate, the reconstruction of the pial surface fails to align correctly with the grey matter boundaries, often (if not always) in the medial temporal lobes. All scans have undergone quality control to include only those with minimal motion artefacts. The age range of the subjects analysed, spans from 0 to 4 years old. All scans were realigned and intensity-corrected using the iBEAT toolbox. We would gladly appreciate any assistance in understanding the causes of this problem and are looking forward to methods or changes that we need to follow in order to solve them. Attached you can find the script we used for the analysis of the scans in a .txt form. Please feel free to ask for any further information, details or materials regarding this issue. Thanks a lot in advance for your time and help! Best regards Thanos Tsigaras ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------ Forschungszentrum Jülich GmbH 52425 Jülich Sitz der Gesellschaft: Jülich Eingetragen im Handelsregister des Amtsgerichts Düren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Stefan Müller Geschäftsführung: Prof. Dr. Astrid Lambrecht (Vorsitzende), Karsten Beneke (stellv. Vorsitzender), Dr. Ir. Pieter Jansens ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------

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Recon-all command produces only 001.mgz file in the mri/orig directory
by Naama Zur 17 Mar '24

17 Mar '24

External Email - Use Caution Hi all, I am using Ubuntu 23.1 with freesurfer 7.4.1 to run the recon-all command and the command runs without error and I do get a set of directories including: label, mri, scripts, stats, surf, tmp, touch, and trash. However, the only folders that are not empty are scripts where there are 11 files and a 001.mgz file in the mri/orig directory. I am not sure what I am doing incorrectly and was hoping for some guidance with this. Thank you!

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Re: [Freesurfer] Large discrepancy in left and right volumes of perirhinal/entorhinal cortices on FreeSurfer 7.1
by Douglas N. Greve 14 Mar '24

14 Mar '24

I've looked into this a little bit. I looked at the area of the original manual labels for entorhinal as found in the aparc. They do show a lh>rh asym of 3%, but it is not significant (p=.45). I looked at the automatic labels in two other large data sets. I found significant lh>rh asym of ento area in both of about 8-10%. I don't consider 10% asym in area to be a symptom of something problematic. This would represent an expansion or contraction of the entorhinal border of about 0.5mm. I'm guessing that this is beyond the accuracy that we can expect. I was looking at surface area, but now I see that you are looking at volume. The manual labels were defined on an areal basis, and I assume that that was the basis of the volume asym, but it could be due to differences in thickness. How big a difference are you seeing in volume? Can you look at area and thickness to see if you see differences there? Also, the surfaces are really hard to place in this area. Oftentimes, the ento will have a big bite in it that has to be fixed manually. I don't think there is asym in the bites, but it could make a particular case look extreme. In general, we don't recommend doing laterality studies with the aparc as none of the steps involved have been developed to make sure that laterality artifacts are removed. In this case, it sounds like you are checking laterality for QA purposes? On 3/13/2024 9:30 PM, Katie Vandeloo wrote: > External Email - Use Caution > > Hi Dr. Greve, > > I hope you are doing well. I am hoping to get in touch with someone from MGH about some issues with Freesurfer 7. Our group hasn’t yet been successful in finding the right person to talk to about this! > > We noticed that there are large discrepancies between left and right hemisphere volumes of the perirhinal cortex (exceptionally small volumes in the right hemisphere) in the outputs of recon-all for Freesurfer 7 but NOT Freesurfer 6. I have reached out to other labs who observed the same pattern. I think there is something systemic about Freesurfer 7 that should be looked into. Just wanted to make someone aware - please let me know if there is someone else I should contact about this. > > Thank you for your time! > > Kind Regards, > Katie Vandeloo

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