Freesurfer February 2023

freesurfer@nmr.mgh.harvard.edu

85 participants
122 discussions

Re: [Freesurfer] Recon-all exited without errors
by Goeckner, Bryna 06 Mar '23

06 Mar '23

External Email - Use Caution Thanks for the response. I should have been more clear in my first email. I have used tkregister2 in the past to fix talairachs, but this one does not appear to be fixable with the in-plane shifting, scaling, and rotating that is available within the tkregister2 GUI. The moveable appears to be in a different plane than the target. I’m attaching a screenshot from tkregister2. Is there a different way to fix the talairach or another recon fix (especially considering the apparent brainmask issue) that should be pursued? Thanks again for your help! Bryna Goeckner (she/her) Graduate Student Meier Lab Medical College of Wisconsin Neuroscience Doctoral Program Date: Fri, 10 Feb 2023 20:48:26 +0000 From: "Huang, Yujing" <YHUANG43(a)mgh.harvard.edu> Subject: Re: [Freesurfer] Recon-all exited with errors To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <MN2PR04MB5982D0100E4EC48D6FD8A2949DDE9(a)MN2PR04MB5982.namprd04.prod.outlook.com> Content-Type: text/plain; charset="us-ascii" Hi Bryna, In this tutorial, it talks about how to fix bad output from the talairach registration: https://secure-web.cisco.com/1AsdowaGUQbpsRB4dUWGRiDD2RdKWB-n1kUwwmPwq1WQ9Y…<https://secure-web.cisco.com/1YTUJIwB-u_KNhoI17IHgKhkMu-K4cxIGnnOeSiooClREn…> Best, Yujing From: freesurfer-bounces(a)nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> On Behalf Of Goeckner, Bryna Sent: Friday, February 10, 2023 3:35 PM To: freesurfer(a)nmr.mgh.harvard.edu Subject: [Freesurfer] Recon-all exited with errors External Email - Use Caution Hi All, I am using FS 7.2.0 and have one subject that exited recon-all with errors (looks like for talairach issues) but I am not able to use tkregister2 to view and make manual adjustments to the talairach since surf/lh.orig was not generated. I then tried recon-all with the -notal-check flag, which exited "without errors" although the talairach is nowhere near correctly aligned and while aparc & aseg in freeview appear ok, the brainmask appears to have issues (when I turn it off, the entire background displays as white). I'm including the recon-all logs (original & notal-check flag) and have listed the actual commands used below as well. Any help you can provide in figuring out how to run this subject is greatly appreciated. Thanks! The original code was: recon-all -subject subj# \ -i rawT1.nii.gz \ -T2 rawT2.nii.gz \ -T2pial \ -parallel -openmp 12 \ -3T \ -all And for the second run, -notal-check was added after -all For tkregister2: tkregister2 --s subj# --fstal --surf orig Bryna Goeckner (she/her) Graduate Student Meier Lab Medical College of Wisconsin Neuroscience Doctoral Program

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Question on mri_nu_correct for 3 Tesla data
by Saemann, Philipp 06 Mar '23

06 Mar '23

External Email - Use Caution Hi FreeSurfer specialists, we have problems with a strong non-intensity in 3 Tesla data of GE (mainly temporal poles and occipital area). We managed to rescue the occipital errors by a pre-Bias-field correction using SPM, but would of course try to optimize this in recon-all itself. When I open the recon-all scrip tin FS v7.1.1 I can find no difference in the parameters depending on if the the flag "-3T" is set or not. In both cases the parameters forwarded are: --n 1 --proto-iters 1000 --distance 50 (in line 1536 and line 1540 of /bin/recon-all.) Could someone explain this? What could be done (manual corrections etc. are obsolete due to the large sample size...) to improve the WM detection in the temporolateral/polar area (subsequently cortex detection)? The brainmask looks okay; the ribbon.mgz shows the cut off lateral parts of the cortex. Thanks in advance for any hints, Philipp

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more detailed instructions for cloning voxels & confirmation that the cloning worked
by Harriott, Emily M 03 Mar '23

03 Mar '23

External Email - Use Caution Dear FS experts, I hope this email finds you all doing well. I am trying to clone voxels back into brainmask.mgz from T1.mgz, but am struggling. I am hoping one of the FS geniuses on here might be able to help me. 1. How exactly do you do it (what do you click on and when, what images do you have active, and what settings are set in the GUI, etc.)? * I read through https://secure-web.cisco.com/1edlOGwMXoyYaTFLL7CtR8DWHAzxHsiS014OXifU0XBn5y… but am not sure it worked so require more detailed instructions that I was unfortunately unable to find on the FreeSurfer website or via google. 2. How do you tell if it worked? I saw https://secure-web.cisco.com/1FkHM4e40vXk3f7s77S0LuFO0Duz3wB6sJb6MPMmOOUvmn… this previous post but it does not seem to have been answered. Any assistance would be greatly appreciated. Thank you so much! All the best, Emily Harriott PhD student, Vanderbilt University

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Neuroimaging postdoctoral fellowship at Stanford University, USA
by Mira Michelle Raman 27 Feb '23

27 Feb '23

External Email - Use Caution Dear FreeSurfer community, The Brain Imaging, Development, and Genetics (BRIDGE) lab, part of Stanford University’s Division of Brain Sciences, is seeking two full-time Postdoctoral Fellows in brain imaging and/or human genetic modeling. Ideal candidates will have a solid neuroscience, neuroimaging, and/or human genetics background. BRIDGE focuses on neuropsychiatric disorders, specifically those associated with RASopathies, such as Noonan syndrome and neurofibromatosis 1 (NF1). In our NIH-funded research, we employ three unique approaches: 1. Taking a genetics-first approach, we study children with known genetic conditions who exhibit attention problems, irritability, and deficits in social cognition. The approach differs from traditional research, which begins with the child's symptoms. 2. We apply in-depth phenotyping of the child's brain, genes, and behavior using brain imaging, genetic testing, and behavioral assessment. 3. We use large publicly available data sets (>10K children) focusing on child brain and behavioral development. Our goal is, therefore, to uncover how genetic variation and its associated downstream pathways affect children's developmental disorders. If interested, please see the official posting for additional details at https://secure-web.cisco.com/1KzHM6M8eHNAqniwUwClGLco44e39zsXfqSw4bO6Ms6b1q… Thank you, Mira Raman, Research Data Analyst BRIDGE, Stanford University

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Consequences of using -notal-check / using a poor talairach transformation
by Tyler Ward 27 Feb '23

27 Feb '23

External Email - Use Caution Hi Freesurfer developers, I am processing several thousand MRIs through Freesurfer and have come across >200 cases where recon-all failed due to the automated talairach QA check. In these cases, I do see some which have bad transformations and others which look acceptable to me. After freesurfer runs, we review the cortical ribbon from the aparc+aseg file to the quality of the parcellation. My question: what problems might arise from using the "-notal-check" on all our freesurfer runs which would not be caught by looking at the parcellation? I am also wondering if you have the "RLB700_preprocessing_statistics.pdf" document which the code references > # now run Avi's QA check on the results found in talairach_avi.log > # see document RLB700_preprocessing_statistics.pdf for details > Thanks for your time, Tyler

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Freeview displaying images in the wrong orientation
by Nathan Kindred (PGR) 27 Feb '23

27 Feb '23

External Email - Use Caution Hi, When I am displaying certain images in freeview the orientation does not match what is displayed in both orient_mri and SPM. The coronal and horizontal views seems to be okay but the midsagittal view is often wrong with the front of the brain tilted up. How do I get freeview to display the images in the correct orientation? Thanks, Nathan

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What's the difference between pc1 and spc (glmfit)
by KennethSPrice 27 Feb '23

27 Feb '23

External Email - Use Caution Hey Freesurfers, I'm running a longitudinal study and have multiple outputs in my results. What's the difference between the "pc1" files and the "spc" files? Also what do the "rate" and "avg" files represent? Any response would be greatly appreciated! Thanks, Ken Sent with [Proton Mail](https://secure-web.cisco.com/1boPq8uQ-9H8Gy1fAGjjCB35J45SPTFBfkpwoo3x… secure email.

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different clusters in mri_surfcluster output versus viewing in Freeview
by Smith, Christine 26 Feb '23

26 Feb '23

External Email - Use Caution Hello, I am getting a mismatch of clusters when we view cluster results in freeview versus ask for a table of the significant clusters. I am performing a GLM analysis on Freesurfer to analyze cortical thickness (mri_glmfit). When viewing the significance map with freeview, we set the minimum threshold to 2 for the sig.mgh file. We also used the same threshold when creating a summary table of the clusters using mri_surfcluster. mri_surfcluster --in {$dir}/visuospatial_MCI_correlation/sig.mgh --hemi left --thmin 2 --thsign pos --minarea 10 --subject fsaverage --surf inflated --annot BN_Atlas --sum {$dir}/visuospatial_MCI_correlation/left.thickness.clustersummary_BN.txt We were hoping to use the summary text file to identify the clusters on freeview and their characteristics (e.g., size, x, y, z ccordinates). Unfortunately, the regions that we see for both methods don’t match as there are some clusters that we see on the summary text file that we don’t see on freeview and vice versa. How can we make the output of these two methods match up? Note that the issue is not the minimum cluster size in the summary table. When we put that to 1 we still get a mismatch. Please note that in the mri_surfcluster program we can indicate that we only want positive results. We don't see a way to do this in freeview or a way for that to affect the p value in freeview. Is this possibly the issue? If so, how can we make a picture in freeview that matches our summary table? Regards, Christine -- Christine N. Smith, Ph.D. Research Service, VA San Diego Healthcare System Department of Psychiatry, University of California San Diego VA San Diego Healthcare System VMRF Building 13 3350 La Jolla Village Drive (151A) San Diego, CA 92161 T: (858) 552-8585; then press *7128

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Re: [Freesurfer] Failing to execute QDEC
by fsbuild 24 Feb '23

24 Feb '23

External Email - Use Caution Hello Vittal, Just FYI, the qdec program is deprecated in 7.X releases and is no longer maintained.  In the 7.X releases, you can try using freeview for images and from the command line there are the mri* commands (mris_surf2surf, mri_glmfit, mri_glmfit-sim, etc.) for stream processing. The license files from older versions of freesrufer, e.g., version 6, are not guaranteed to work on newer versions of linux OS’s because of changes to the crypt libraries.  But a new license should work with a 7.X release. Please in the future do not post any license files or content from them to the public mailing list.  We can instruct you how to otherwise upload files for us to view. - R. On Feb 24, 2023, at 12:15, Wighton, Paul <PWIGHTON(a)mgh.harvard.edu> wrote:Hi Vittal,I tested your license file and it's fine.  Are you sure it's in the right place?  What's the output of `cat /usr/local/freesurfer/license.txt`?It also looks like QDEC is trying to write to `/usr/local/freesurfer/subjects/qdec/Untitled/contrasts.sig.mgh` do you have permissions to write there?  I'd suggest creating a FreeSurfer subjects directory under your home and setting the SUBJECTS_DIR environment variable accordingly, e.g.mkdir ~/fs-subjectsexport SUBJECTS_DIR="${HOME}/fs-subjects"-Paul________________________________________From: freesurfer-bounces(a)nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of vittal korann <vittalkorann(a)gmail.com>Sent: Friday, February 24, 2023 11:56 AMTo: Freesurfer support listSubject: Re: [Freesurfer] Failing to execute QDEC       External Email - Use CautionHi Freesurfer experts,I am looking forward to resolve this issue.Any help would be greatly appreciated!With regards,VittalOn Wed, Feb 22, 2023 at 3:13 PM vittal korann <vittalkorann@gmail.com<mailto:vittalkorann@gmail.com>> wrote:Hi Freesurfer experts,I am trying to run Qdec on schizophrenia pre and post intervention scans.I created .dat and .levels  files within the qdec folders and loaded the .dat file into qdec gui.It is suddenly crashing when I select my design and hit the Analyze button.And the same error message copied below from the terminal.Writing to /usr/local/freesurfer/subjects/qdec/Untitled/contrasts.sig.mgh--------------------------------------------------------------------------ERROR: Invalid FreeSurfer license key found in license file /usr/local/freesurfer/license.txt If you are outside the NMR-Martinos Center, go to MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://secure-web.cisco.com/1nLzKBZWbv5Bmrf0Y03boA8pp7LUIugSlf4PhO_BVoRF79s… to get a valid license file (it's free). If you are inside the NMR-Martinos Center, make sure to source the standard environment.Even though I renewed my license file, the issue still persists.FYI I did use qdec in the past and am quite comfortable with it.Also, I attached my license file if anything is missing.Any help would be appreciated!With regardsVittal_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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7.3.2-patch issues - thalamic segmentation
by Katie Rose Jobson 24 Feb '23

24 Feb '23

External Email - Use Caution Hi FS experts, I am attempting to implement the patch on version 7.3.2 for issues with thalamic segmentation. I followed the instructions found here: https://secure-web.cisco.com/1JULaWPox6hiL5oNotdoE4us3D1hhs0HqpeHRUYFRvLuHP… and placed the scripts in their designated directories. However, I received the same error as before. The output indicates that the core.py script is located in the '$FREESURFER/python/packages/freesurfer/subregions/' directory, as opposed to the directory I was instructed to put the core.py script in ('$FREESURFER/python/packages/gems/subregions/'). Should I replace the core.py script within '$FREESURFER/python/packages/freesurfer/subregions/'? Or is there another course of action that I can do that may solve this issue? Here is the exact error, if that is at all helpful: Step 2: aligning atlas to reference segmentation Traceback (most recent call last): File "/usr/local/freesurfer-7.3.2/python/scripts/segment_subregions", line 99, in <module> subregions.run_cross_sectional(args.structure, parameters) File "/usr/local/freesurfer-7.3.2/python/packages/freesurfer/subregions/process.py", line 52, in run_cross_sectional model.align_atlas_to_seg() File "/usr/local/freesurfer-7.3.2/python/packages/freesurfer/subregions/core.py", line 240, in align_atlas_to_seg mask = mask.resize(1, interp='nearest') TypeError: resize() got an unexpected keyword argument 'interp' Thank you in advance for your help! Best Wishes, Katie -- Katie Jobson, M.S. | Personal Website<https://secure-web.cisco.com/1pn78j_bRtnBgT0xpSoaIHzF2FCTjom5RSQL5Coy-3athV…> Ph.D. Student | Cognitive Neuroscience Lab<https://secure-web.cisco.com/13fFt8PE3xjBFNhyYO17_fs-djBanSzBziNRRKhkYNAIjV…> Department of Psychology and Neuroscience | Temple University

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Freesurfer February 2023