[Freesurfer] intensity map
External Email - Use Caution Dear Freesurfer experts,I have some questions about intensity map: 1. If I would like to get intensity maps of WM, which were created at 1 mm below the white surface, and the GM were taken at half of the thickness of the cortex. which commands I can use. 2. How to use the command line to get the Grey-matter tissue intensity at 10% up to 60% of the distance from the white matter to the pial surface. 3. Then, how to get the WM/GM intensity maps use the above values. Best regards, Zhang Xia ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] TRACULA question: Preprocessing exited with ERRORS
External Email - Use Caution Dear Freesurfer experts, I am a beginner in the use of TRACULA. I tried to run the preprocessing step of the trac-all command and it seems that all have worked fine. However, at the end of the command TRACULA finished with an error. This is the final output tkregister2 --mov /Applications/freesurfer_dev/freesurfer/subjects/TUTORIAL_DATA/4220/4220/4220/dmri/brain_anat_orig.nii.gz --targ /Applications/freesurfer_dev/freesurfer/subjects/TUTORIAL_DATA/4220/4220/4220/dmri/brain_anat.nii.gz --regheader --noedit --fslregout /Applications/freesurfer_dev/freesurfer/subjects/TUTORIAL_DATA/4220/4220/4220/dmri/xfms/anatorig2anat.mat --reg /Applications/freesurfer_dev/freesurfer/subjects/TUTORIAL_DATA/4220/4220/4220/dmri/xfms/anat2anatorig.dat tkregister2: Command not found. Darwin rmnlab1.inv.usc.es 17.7.0 Darwin Kernel Version 17.7.0: Thu Jun 21 22:53:14 PDT 2018; root:xnu-4570.71.2~1/RELEASE_X86_64 x86_64 trac-preproc exited with ERRORS at Mon Dec 9 22:00:14 CET 2019 You can find the configuration file and the trac-all.log file in attached. Best regards, -- *Miguel Ángel Rivas Fernández* trac-all.log Description: Binary data dmrirc.tutorial Description: Binary data ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Recon-all
can you check to see if there is a large defect that is too big to fix? You should be able to see this in the log file or by checking the output of the job it is waiting for (PID 175414) On Tue, 10 Dec 2019, Gwang-Won Kim wrote: External Email - Use Caution Hi there, I tried to process "recon-all" as follow: recon-all -autorecon-all -i A.nii.gz -s A -parallel But, there is the message for 4 days as follow (FREESURFER _HOME /usr/local/freesurfer/dev): #@# Fix Topology rh mris_fix_topology -maz -sphere qsphere.nofix -inflated inflated.nofix -orig orig.nofix -out orig -ga -seed 1234 A rh Waiting for PID 175414 of (175414 175417) to complete... [?usn=6394937=kw0...@nate.com=cdb2d038f8e5c2bc28e1c728b8f131da$64cb4...@mail3.nate.com] ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Recon-all
External Email - Use CautionHi there, I tried to process "recon-all" as follow: recon-all -autorecon-all -i A.nii.gz -s A -parallel But, there is the message for 4 days as follow (FREESURFER _HOME /usr/local/freesurfer/dev):#@# Fix Topology rhmris_fix_topology -maz -sphere qsphere.nofix -inflated inflated.nofix -orig orig.nofix -out orig -ga -seed 1234 A rhWaiting for PID 175414 of (175414 175417) to complete... ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] "Bad CPU type in executable" error
There is also tkregisterfv, which takes all the same arguments as tkregister2 but uses freeview instead On 12/9/19 1:39 PM, Hoopes, Andrew wrote: > Hi Abhi, > > The tkregister GUI built for v6 is no longer supported on modern macs since > it's a 32-bit program, which Catalina will not run. If you're just trying to > run a registration, you should be able to use tkregister2_cmdl without any > issues. For visualization, I recommend switching to freeview. > > best > Andrew > > > From: freesurfer-boun...@nmr.mgh.harvard.edu > on behalf of Abhi Jaywant > > Sent: Monday, December 9, 2019 1:29 PM > To: freesurfer@nmr.mgh.harvard.edu > Subject: [Freesurfer] "Bad CPU type in executable" error > > External Email - Use Caution > > Hi, > > I am trying to run the tkregister2.bin script and receive the following > error: Bad CPU type in executable. > > I see that this question was asked some time back and it sounded like it > might be a Mac OS version issue? I am running macOS Catalina 10.15.1 and > Freesurfer version 6 (freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c) > > Thank you, > Abhi > -- > Abhishek Jaywant, Ph.D. > Assistant Professor of Neuropsychology, Weill Cornell Medicine > Assistant Attending Psychologist, NewYork-Presbyterian Hospital > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] "Bad CPU type in executable" error
Hi Abhi, The tkregister GUI built for v6 is no longer supported on modern macs since it's a 32-bit program, which Catalina will not run. If you're just trying to run a registration, you should be able to use tkregister2_cmdl without any issues. For visualization, I recommend switching to freeview. best Andrew From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Abhi Jaywant Sent: Monday, December 9, 2019 1:29 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] "Bad CPU type in executable" error External Email - Use Caution Hi, I am trying to run the tkregister2.bin script and receive the following error: Bad CPU type in executable. I see that this question was asked some time back and it sounded like it might be a Mac OS version issue? I am running macOS Catalina 10.15.1 and Freesurfer version 6 (freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c) Thank you, Abhi -- Abhishek Jaywant, Ph.D. Assistant Professor of Neuropsychology, Weill Cornell Medicine Assistant Attending Psychologist, NewYork-Presbyterian Hospital ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] "Bad CPU type in executable" error
External Email - Use Caution Hi, I am trying to run the tkregister2.bin script and receive the following error: Bad CPU type in executable. I see that this question was asked some time back and it sounded like it might be a Mac OS version issue? I am running macOS Catalina 10.15.1 and Freesurfer version 6 (freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c) Thank you, Abhi -- Abhishek Jaywant, Ph.D. Assistant Professor of Neuropsychology, Weill Cornell Medicine Assistant Attending Psychologist, NewYork-Presbyterian Hospital ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Vertex-wise ROI extractions on the surface
You can create a mask of the ROI using mri_annotation2label using the --seg output. Then create a mask with mri_binarize --i seg.nii.gz --match MATCHVAL --o mask.nii.gz where MATCHVAL is the ID of your ROI from $FREESURFER_HOME/FreeSurferColorLUT.txt You can then use the fslmeants command below. The one problem that might occur is that FS uses an extention to nifti that allows it to represent surface-based data. FSL might not be able to read this. If so, we can find a work-around On 12/8/19 1:03 AM, DeCross, Stephanie N. wrote: > Hi, > > How can I extract functional data (percent contrast) from an aparc ROI on the > surface on a vertex-wise basis (i.e. not one value averaged across the whole > ROI, but one value per vertex inside the ROI for a given contrast)? > Funcroi-config/funcroi-sess/funcroi-table-sess seem to only provide values > averaged across the whole ROI. > > In other analysis pipelines, for a voxel-wise extraction it looks like I > would use > $ fslmeants -i -o -m <3D mask nii> --showall > but I’m not sure how to do this on the surface. > > Thank you, > Stephanie DeCross > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] fsaverage for externally preprocessed subjects.
On 12/7/19 5:42 PM, Alvarado,Luis R wrote: > > External Email - Use Caution > > Hi all, > > I have a couple of questions regarding fsaverage: > > 1. Is this file updated every time a new subject is process with > recon-all? > No, fsaverage will not be changed. > > 1. If I obtain externally preprocessed datasets (e.g., from the 1000 > Functional Connectomes Project) should I register those subjects > to my local fsaverage? > Not sure what you mean. If you run the 1kFC anatomical data through recon-all, they will automatically be registered > > 1. > 1. Ultimately, I would like to conduct an ROI analysis of the > differences between normative data from a large online biobank > and locally imaged patient population. The workflow for such > analysis recommended on > (https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/AnatomicalROI) > suggests to draw ROI labels directly on fsaverage (*/_a > template to which all subjects run with FreeSurfer have been > registered to_/*) and then use the mri_label2label command to > map the label to individual subjects. Would this work for both > locally and externally preprocessed groups? > Yes > 1. > > Thank you, > > Luis R. Alvarado > > Ph.D. Candidate > > Department of Anatomical Sciences and Neurobiology > > University of Louisville School of Medicine > > Kentucky Spinal Cord Injury Research Center > > 220 Abraham Flexner Way, Suite 1500 > > Louisville, KY 40202 > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Reconstruction on BLADE sequences
External Email - Use Caution Freesurfer experts, We're attempting to get some reconstructions on MRI's for very advanced alzheimer's subjects. Many of these subjects have pretty extensive motion artifacts in their acquisitions. There has been some work with the so-called BLADE sequences to eliminate motion. Indeed, some of the blade sequences produce fairly good contrast. But these acquisitions have slices that aren't normalized for brightness and I think this complicates the reconstruction--see ( https://imgur.com/ZWhBlcm ) for an example. It seems like we should be able to perform some kind of slice-wise normalization to fix this, but I can't see a good way to do that with the freesurfer tools. Any advice would be greatly appreciated! Quentin Funk, PhD Houston Methodist Research Institute 713-363-9003 Houston Methodist. Leading Medicine. Houston Methodist is ranked by U.S. News & World Report as the No. 1 hospital in Texas and among the top 20 hospitals nationwide. Houston Methodist is the only nationally ranked Honor Roll hospital in the state and is designated as a Magnet hospital for excellence in nursing. 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. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] PETSurfer individual atlas for subcortocal segmentation
External Email - Use Caution Dear Doug, thank you for your effort. Let me know if you have any updates on this. Best, Boris On Fri, Dec 6, 2019 at 5:45 PM Greve, Douglas N.,Ph.D. < dgr...@mgh.harvard.edu> wrote: > Hi Boris, I'll try to get to it today. Unfortunately, I think this is > going to require a fair amount of effort on my part. When I wrote this part > of PETsurfer, I just did not make it super flexible. > doug > > > On 12/5/2019 10:17 PM, Boris Rauchmann wrote: > > External Email - Use Caution > Did you already have the time to look at the logfile? Do you have any > suggestions how to proceed? > > Thank you! > > Am 02.12.2019 um 19:18 schrieb Boris Rauchmann > : > > > In this example tried it with only the subcortical segmentations from my > atlas. Please find the logfile attached. It gives me back: "tissue type is > not set" but I set it to 2 in the LUT.txt > > In principle look the following commands right to you? > > xcerebralseg --s 0120test --o apas+head+subcort_BN.mgz --m > BN_Atlas_subcotex.mgz --atlas BN_Atlas_subcortex.gca > > gtmseg --s 0120test --head apas+head+subcort_BN.mgz --ctab > subcort_BN_LUT.txt --o gtmseg+subcort_BN.mgz > > Ideally I would have a gtmseg with both, the subcortical and the cortical > structures, but only the subcortical would also be fine as long as I can > get mri_gtmpvc running on it. > > Thanks, > Boris > > On Mon, Dec 2, 2019 at 5:31 PM Greve, Douglas N.,Ph.D. < > dgr...@mgh.harvard.edu> wrote: > >> Can you send the log file for each of the gtmseg runs? >> >> On 11/26/2019 1:09 PM, Boris Rauchmann wrote: >> >> External Email - Use Caution >> Thank you! I have a gca for subcortical and two gcs (lh/rh) for cortical >> structures. >> I created an annot (rh/lh) and a mgz using mris_ca_label and mri_ca_label >> for parcellation/segmentation stats. >> >> For the PET analysis I have the following problem: >> >> If I use this command: gtmseg --s test --o test.mgz --ctab >> /xyz/BN_Atlas_246_LUT.txt --head BN_Atlas_subcotex.mgz --ctx-annot >> BN_Atlas.annot --ctab '/xyz/BN_Atlas_246_LUT.txt' >> >> It gives me the right regions for subcortical structures but it looks >> like it uses the standard FS parcellation with my labels for the cortical >> parcellations (only 93 cortical regions instead of 210). >> >> If I use gtmseg --s 0059test --o onlyhead.gtmseg_test.mgz --ctx-annot >> BN_Atlas.annot --ctab '/xyz/BN_Atlas_246_LUT.txt' --no-xcerseg I get all my >> 210 cortical parcellations but the standard FS subcortical segmentations. >> >> How can I use both in one gtmseg so that I can proceed with it doing my >> PET analysis in PETSurfer? It is not totally clear for me what to merge >> using xcerebralseg. >> >> Thanks a lot! >> >> On Mon, Nov 18, 2019 at 8:28 PM Greve, Douglas N.,Ph.D. < >> dgr...@mgh.harvard.edu> wrote: >> >>> It gets the subcortical from apas+head.mgz which gets created along the >>> way by xcerebralseg. You can create your own with xcerebralseg by >>> specifying your volume as the mergevol. I think this will work, but I'm >>> not sure. I'm assuming you've used the GCA to create your own >>> subcortical seg for the given subject >>> >>> On 11/5/19 1:06 PM, Boris Rauchmann wrote: >>> > >>> > External Email - Use Caution >>> > >>> > I just realized that the above mentioned command (gtmseg --s XYZ --o >>> > BN.gtmseg.mgz --ctx-annot BN_Atlas.annot --ctab >>> > '/media/XYZ/BN_Atlas_freesurfer/BN_Atlas_246_LUT.txt' --no-xcerseg) >>> > gives me only the cortical segmentation. Is there any way to also >>> > include the subcortical segmentation based on my individual atlas? I >>> > also have an Atlas_subcortex.gca file available. >>> > >>> > Best, >>> > Boris >>> > >>> > On Tue, Aug 13, 2019 at 5:10 PM Greve, Douglas N.,Ph.D. >>> > mailto:dgr...@mgh.harvard.edu>> wrote: >>> > >>> > There is no cut off for the minimum size. As it gets smaller, the >>> PVC >>> > noise amplification will become bigger (it also depends on the >>> > shape as >>> > well). >>> > >>> > I think the --no-xcerseg is the right way to go now >>> > >>> > On 8/13/19 11:00 AM, Boris Rauchmann wrote: >>> > > >>> > > External Email - Use Caution >>> > > >>> > > Thank you for your prompt answer - the command worked. This is >>> the >>> > > atlas mentioned: http://atlas.brainnetome.org/brainnetome.html >>> > > What is approximately the smallest possible segment when using >>> PVC? >>> > > Also, does the exclusion of extracerebral structures harm? I >>> > used that >>> > > flag because it complained: >>> > > >>> > > gtmseg --s XYZ --o BN.gtmseg.mgz --ctx-annot BN_Atlas.annot >>> --ctab >>> > > '/media/XYZ/BN_Atlas_freesurfer/BN_Atlas_246_LUT.txt' >>> > > ERROR: /media/subjects/XYZ/mri/apas+head.mgz exists. This is ok >>> > > but you must indicate whether to use what is there (--no-xcerseg) >>> > > or create a new one and overwrite what is there (--xcerseg)
