Freesurfer

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30085 discussions

Help to create flattened images of the whole brain
by Ornaith O Reilly 21 Oct '20

21 Oct '20

External Email - Use Caution Hello Freesurfer developers, I am new to Freesurfer and I'm hoping that someone can help me; I'm attempting to get a flattened patch of an entire hemisphere. Below is a page outlining how to use mris_flatten to achieve this: https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferOccipitalFlattenedPatch I am just trying to achieve this with the tutorial data to start with. 1. First problem is that when I run the command 'tksurferfv bert lh inflated'; I am getting the error outlined in Image 1. 2. I realised that I could create a patch using freeview instead of tksurfer. However I attempted to follow the instructions on the page above to do this and ran into some problems. Image 2 shows an example of the patch that I created and image 3 shows the error that I get when I attempt to press the Press Fill Uncut Area button (I tried this many times and got the same result). 3. However one time I did succeed in making a patch (I don't know what I did differently this time?) - see image 4 attached. I saved it as lh.full.patch.3d. When I tried to run the command mris_flatten below I got the error outlined in image 5. mris_flatten -w 10 lh.full.patch.3d lh.full.flat.patch.3d The version of Freesurfer and the platform that I'm using is outlined below: 1) FreeSurfer version: freesurfer-darwin-macOS-7.1.1-20200811-8b40551 2) Platform: macOS High Sierra 10.13.6 (17G7024) If anyone could shed some light on any of these errors or suggest an alternative method it would be greatly appreciated. Thanks a lot. Kind Regards Ornaith O'Reilly

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Estimating the memory footprint of Longitudinal Stream?
by Paul Wighton 21 Oct '20

21 Oct '20

External Email - Use Caution Hi FreeSurfers, Is there any guidance on how to estimate the memory footprint of the Longitudinal steam? We are trying to process the MacLaren test-retest dataset [1] (40 timepoints per subject) with the longitudinal stream in v7.1.1 and are running into memory errors during `mri_fuse_segmentations`. Thanks, -Paul [1]: https://openneuro.org/datasets/ds000239/versions/00001

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replace the vertex_label_index in .annot file
by 1248742467 20 Oct '20

20 Oct '20

External Email - Use Caution hello, Previously, rh.white and rh.aparc.2009s.annot were used to generate vertex_id and vertex_label,  ' from freesurfer_surface import Surface from freesurfer_surface import Label from freesurfer_surface import Annotation surface = Surface.read_triangular('rh.white') surface.load_annotation_file('rh.aparc.a2009s.annot') with open("rhlabels.txt","w") as f: for vertex_index, vertex in enumerate(surface.vertices): vertex_label_index = surface.annotation.vertex_label_index[vertex_index] vertex_label = surface.annotation.labels[vertex_label_index] #print(vertex_index, vertex, vertex_label) #f.write("vertex_index:{} vertexlabel:{} \n".format(vertex_index, vertex_label)) f.write("vertex_index:{} vertex_label:{}\n".format(vertex_index, vertex_label)) ' the output:vertex_index:0 vertexlabel:Label(name=S_precentral-sup-part, index=70, color=#1514c8) and the label_index obtained after a certain algorithm was updated to replace the vertex_labe_index in rh.aparc.2009s.annot, and then load the result with freeview. But I don't know how to replace the vertex_label_index value in .annot? 

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white and pial surfaces appearing outside gray matter boundary
by Batool Rizvi 20 Oct '20

20 Oct '20

External Email - Use Caution Dear FreeSurfer experts, I wrote in this question around a week ago, but haven't heard back. I'm attempting again without attaching an image, since I didn't see this getting posted the first time. I'm seeing this type of error reoccur for around half of the subjects I've reviewed so far for a study. The pial and white surfaces are merging to the outermost boundary of the brain, and almost completely overlapping each other. Provided that these are older subjects, but I didn't see this error in my experience editing older subjects in other studies. Is there perhaps a preprocessing command I could perform since this error is systematic throughout the brain, not specific to a region? I tried segmenting out the dura/CSF, and rerunning with a cleaner brain mask, and that helped a little but not too much. I also tried running it with a T2 input, but that also didn't fix the issue, though there was a little improvement;. Trying to run it with a FLAIR now, since the T2 didn't include the whole brain. Thank you for any input! Batool

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Error running mris_ca_label
by Rollo, Patrick 20 Oct '20

20 Oct '20

External Email - Use Caution Experts, My group runs an older version of Freesurfer so that when we run recon-all, it creates the 2005 FS atlas. I've installed the current version of FS on a new machine and I'm trying to go back and create DKT atlases for each of our previous patients. I use the following code, hoping to generate an .annot file but get the following output: mris_ca_label ../label/lh.cortex.label -aseg aseg.presurf.mgz < subjid > lh ../surf/lh.sphere.reg /Applications/freesurfer/average/lh.DKTatlas40.gcs ../label/lh/aparc.DKTatlas.annot GCSAread(../surf/lh.sphere.reg): file magic #fffffe63 != GCSA_MAGIC (ababcdcd) mris_ca_label: could not read classifier from ../surf/lh.sphere.reg if I run it without the file path for the lh.sphere.reg file I get the following: mris_ca_label ../label/lh.cortex.label -aseg aseg.presurf.mgz < subjid > lh lh.sphere.reg /Applications/freesurfer/average/lh.DKTatlas40.gcs ../label/lh/aparc.DKTatlas.annot GCSAread(lh.sphere.reg): could not open file No such file or directory mris_ca_label: could not read classifier from lh.sphere.reg No such file or directory Thank you for your help!

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Error during skullstripping: numerical result out of range
by Hye Min Shin 20 Oct '20

20 Oct '20

External Email - Use Caution Hi experts, While running recon-all on subjects with 3T T1 scans, I ran into an error with one subject during skullstripping stage. Recon-all was running with 3T flag. The error message is the following: register_mri: find_optimal_transform find_optimal_transform: nsamples 3243, passno 0, spacing 8 GCAhistoScaleImageIntensities: could not find wm peak resetting wm mean[0]: 100 --> 108 resetting gm mean[0]: 61 --> 61 input volume #1 is the most T1-like using real data threshold=10.0 skull bounding box = (46, 56, 29) --> (216, 255, 255) using (103, 122, 142) as brain centroid... mean wm in atlas = 108, using box (82,97,114) --> (123, 146,169) to find MRI wm before smoothing, mri peak at 73 robust fit to distribution - 72 +- 7.4 distribution too broad for accurate scaling - disabling WARNING2: gca.c::GCAhistoScaleImageIntensities: h_mri->nbins=100, mri_peak=108 after smoothing, mri peak at 0, scaling input intensities by inf Numerical result out of range I tried the following suggestion in https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg12605.html but to no avail. It's just strange because only one subject has this issue and the subject's scan looks fine- no part of the brain seems cutoff. Any suggestions would be helpful. Best, Julia Shin

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Re: [Freesurfer] Problem with dcmunpack on freesurfer
by fsbuild 20 Oct '20

20 Oct '20

External Email - Use Caution Hello Praveen, The first line of dcmunpack script should indicate it calls the tcsh interpreter.  However, neither csh or tcsh interpreters are installed by default on Ubuntu.  The "which" command will probably report it is not found on your system thru your $PATH. $ which tcsh tcsh: Command not found But you can install the C shells manually via, $ sudo apt-get install tcsh csh .... after the install try the which command again. I am a working on a debian installer package so these manual installs will no longer be necessary. - R. On Oct 20, 2020, at 01:10, Praveen Raghunathan <praveenvr28(a)gmail.com> wrote:        External Email - Use Caution        Hi Freesurfer developers,Sorry if I'm making a simple mistake that I've overlooked. I am currently trying to do the freesurfer tutorials available at http://surfer.nmr.mgh.harvard.edu/fswiki/Tutorialsand am having problems with the dcmunpack command on freesurfer. Whenever I try to run the dcmunpack script (whether it's dcmunpack -help or dcmunpack -src . -scanonly scan.log), I get the following error message :bash: /home/praveen/freesurfer/bin/dcmunpack: /bin/tcsh: bad interpreter: No such file or directoryI have installed freesurfer, added the license and am able to use freeview to open .mgz and .pial files so I'm not sure why dcmunpack is missing. I'm not able to find any online documentation on how to install or source that particular script either. I've searched the list archive and no similar errors have been reported. Please advise and let me know what I should do or what I'm doing wrong.I am currently running freesurfer on a virtual machine using Oracle Virtualbox 6.1 on my Windows laptop. The OS on the virtual machine I'm using is:Ubuntu 20.04.1 LTS and the freesurfer version is: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551I am using a Bash shell to run the commands.Thank you so much for your help! Please let me know if you need any other information.SincerelyPraveen V. Raghunathan_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Problem with dcmunpack on freesurfer
by Praveen Raghunathan 20 Oct '20

20 Oct '20

External Email - Use Caution Hi Freesurfer developers, Sorry if I'm making a simple mistake that I've overlooked. I am currently trying to do the freesurfer tutorials available at http://surfer.nmr.mgh.harvard.edu/fswiki/Tutorials and am having problems with the dcmunpack command on freesurfer. Whenever I try to run the dcmunpack script (whether it's dcmunpack -help or dcmunpack -src . -scanonly scan.log), I get the following error message : bash: /home/praveen/freesurfer/bin/dcmunpack: /bin/tcsh: bad interpreter: No such file or directory I have installed freesurfer, added the license and am able to use freeview to open .mgz and .pial files so I'm not sure why dcmunpack is missing. I'm not able to find any online documentation on how to install or source that particular script either. I've searched the list archive and no similar errors have been reported. Please advise and let me know what I should do or what I'm doing wrong. I am currently running freesurfer on a virtual machine using Oracle Virtualbox 6.1 on my Windows laptop. The OS on the virtual machine I'm using is: Ubuntu 20.04.1 LTS and the freesurfer version is: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 I am using a Bash shell to run the commands. Thank you so much for your help! Please let me know if you need any other information. Sincerely Praveen V. Raghunathan

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why can't I receive a reply from others in my mailbox?
by 1248742467 19 Oct '20

19 Oct '20

External Email - Use Caution Hello,  After i asked a question, why can't I receive a reply from others in my mailbox?

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mkanalysis-sess and mkcontrast-sess scripts for FIR analysis
by Fang, Angela,Ph.D. 19 Oct '20

19 Oct '20

Hello Freesurfer community, I am trying to configure first level FIR analyses and contrasts for an event related task based on the design in the attached paper. I have 3 conditions (self, other, case) plus fixation. I believe the time window is 30 sec with 11 frames, 12 time points and the TR = 2.5 sec: Timecourse: -5 -2.5 0 2.5 5 7.5 10 12.5 15 17.5 20 25 Timepoint: 0 1 2 3 4 5 6 7 8 9 10 11 The paradigm file for 1 of my 3 runs (attached) was developed using Optseq with Doug’s help, and I believe the TER in this case would be 2.5 sec. Do the following commands look correct? mkanalysis-sess -analysis selfotherfir.lh -TR 2.5 -refeventdur 2.5 -paradigm self.other.par -event-related -fsd bold -surface fsaverage lh -nconditions 3 -timewindow 30 -fir 5 30 -TER 2.5 -per-run mkcontrast-sess -analysis selfotherfir.lh -contrast self-v-other -a 1 -c 3 -no-sumdelays -rmprestim I want to be able to view timecourses at each time point (hence the -no-sumdelays flag) in tksurfer (or freeview) but I am not sure about using the -rmprestim flag. Is there any instance when I would not want to remove baseline shifts? Thanks for your help! Angela Angela Fang, Ph.D. Assistant Professor of Psychology, Harvard Medical School Department of Psychiatry, Massachusetts General Hospital OCD and Related Disorders Program 185 Cambridge Street, Suite 2000 Boston, MA 02114 Email: afang(a)mgh.harvard.edu<mailto:afang@mgh.harvard.edu> Phone: (617) 643-7717 Fax: (617) 643-3080

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