Freesurfer February 2022

freesurfer@nmr.mgh.harvard.edu

83 participants
132 discussions

mri_glmfit error: MatrixMultiplyD(): m2 is null
by 정현우 10 Mar '22

10 Mar '22

External Email - Use Caution Hello FreeSurfer Developers, I'm attempting to compare cortical surface area among three groups while controlling for estimated total intracranial volume (eTIV), as described on the Surface Based Group Analysis tutorial ( https://secure-web.cisco.com/1A0QSPCwnovVVVsFNKDP8OXxiBFqZ78jELzRvCgQt7us3r… I ran the following command: mri_glmfit --y three_group_comparison.area.lh.10.mgh --fsgd three_group_comparison.area.fsgd dods --C three_group_comparison.area.mtx --surf fsaverage lh --cortex --glmdir three_group_comparison.area.lh.glmdir --eres-save Then I got the following error: gdfRead(): reading three_group_comparison.area.fsgd INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done. Continuous Variable Means (all subjects) 0 eTIV 1.53351e+06 139455 Class Size and Means of each Continuous Variable 1 0 42 1566070.5417 2 1 34 1515147.1360 3 2 15 1483959.5000 INFO: gd2mtx_method is dods Reading source surface /media/sjkim/hd2/subject_data/fsaverage/surf/lh.white Number of vertices 163842 Number of faces 327680 Total area 65417.000000 AvgVtxArea 0.399269 AvgVtxDist 0.721953 StdVtxDist 0.195472 7.2.0 cwd /media/sjkim/hd2/subject_data/glm cmdline mri_glmfit --y three_group_comparison.area.lh.10.mgh --fsgd three_group_comparison.area.fsgd dods --C three_group_comparison.area.mtx --surf fsaverage lh --cortex --glmdir three_group_comparison.area.lh.glmdir --eres-save sysname Linux hostname sjkim-System-Product-Name machine x86_64 user sjkim FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 0 y /media/sjkim/hd2/subject_data/glm/three_group_comparison.area.lh.10.mgh logyflag 0 usedti 0 FSGD three_group_comparison.area.fsgd labelmask /media/sjkim/hd2/subject_data/fsaverage/label/lh.cortex.label maskinv 0 glmdir three_group_comparison.area.lh.glmdir IllCondOK 0 ReScaleX 1 DoFFx 0 Creating output directory three_group_comparison.area.lh.glmdir Loading y from /media/sjkim/hd2/subject_data/glm/three_group_comparison.area.lh.10.mgh ... done reading. INFO: gd2mtx_method is dods Saving design matrix to three_group_comparison.area.lh.glmdir/Xg.dat Computing normalized matrix Normalized matrix condition is 833.575 Matrix condition is 1e+08 Found 149955 points in label. Pruning voxels by thr: 1.175494e-38 Found 149953 voxels in mask Saving mask to three_group_comparison.area.lh.glmdir/mask.mgh Reshaping mriglm->mask... search space = 74612.059149 DOF = 85 Starting fit and test Fit completed in 0.0373833 minutes Computing spatial AR1 on surface Residual: ar1mn=0.997826, ar1std=0.000886, gstd=8.674183, fwhm=20.426140 Writing results three_group_comparison.area maxvox sig=3.0263 F=7.57212 at index 107440 0 0 seed=1645215319 error: No such file or directory error: MatrixMultiplyD(): m2 is null break /home/rd521/space_freesurfer/build/docker_ubuntu18/trunk/rd521-7.2.0/utils/matrix.cpp:596 I used FreeSurfer version 7.2.0 and Ubuntu 20.04. I've searched the mail archives and similar errors have been reported in qdec, but I could not find any specific solution for this problem. Do you have any suggestions to solve this problem? Thank you in advance, Hyunwoo Jeong

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Checking for (invalid) multi-frame inputs... ERROR: input(s) cannot have multiple frames!
by Knut J Bjuland 02 Mar '22

02 Mar '22

External Email - Use Caution Dear Freesurfer experts, I get this error when I am running FreeSurfer. Checking for (invalid) multi-frame inputs... ERROR: input(s) cannot have multiple frames! /home/knutjb/subjects/test/mri/orig/001.mgz has 4 frames If this is a multi-frame MEMPRAGE image, use mri_concat --rms to combine echo frames. It has a t1_sag_mprage sequence, and it also give this waning filesare not found to be different and cannot be sorted. In addition, I get these errors when importing using recon-all -i file -all -s test INFO: Found 770 files in //20210224_151919/5_t1_sag_mprage INFO: Scanning for Series Number 5 Scanning Directory INFO: found 768 files in series INFO: loading series header info. When I am running mri_concat --rms I am able to run recon-all -all. Your sincerely, Knut Jørgen Bjuland

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Re: [Freesurfer] SAMSEG "lesion" (Illegal instruction) ~ running VM_67
by Cerri, Stefano 28 Feb '22

28 Feb '22

Hi Randy, Your run_samseg syntax is correct and yes, the "lesion" version of SAMSEG requires Tensorflow. The "illegal instruction" error is most probably related to an incompatible version of Tensorflow with your CPU instruction set. You should be able to replicate the error by typing: 1. fspython 1. import tensorflow Would you be able to run SAMSEG lesion on another host machine (possibly a relatively new one) and let us know if the error persists? Best, Stefano Dear R, Yes, I have tried to run "samseg_run" from the command line (I've repeated my syntax below).? I have looked both under the directory where the command ran that produced the ?Illegal instruction? error.? No crash file (a logfile?) or a "core" file were written.? I also looked?/var/crash but that folder was empty too. As I mentioned, I'm a LINUX novice.? I'm even more of a novice with regard to Python. However, I did take a quick at the code looking for any mention of tensorflow, and have copied the python script text as it exists below.? I have highlighted the only mention of tensorflow below.? Does this look like you expect it? Has tensorflow actually been incorporated into the VM??? Note that I have been able to successfully run Samseg without the --lesion flag and the process works just fine (about 20min runtime, aseg looks just fine in Freeview) Again, thanks for any guidance you can provide. -Randy xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx #!/usr/bin/env python import osimport sysimport jsonimport scipy.ioimport freesurfer as fsimport freesurfer.samseg as samseg # ------ Parse Command Line Arguments ------ parser = fs.utils.ArgumentParser() default_threads = int(os.environ.get('OMP_NUM_THREADS', 1)) # requiredparser.add_argument('-o', '--output', metavar='DIR', dest='outputDirectory', help='Output directory.', required=True)parser.add_argument('-i', '--input', nargs='+', action='extend', metavar='FILE', dest='inputFileNames', help='Input image(s).', required=True)# optional processing optionsparser.add_argument('-m', '--mode', nargs='+', help='Output basenames for the input image mode.')parser.add_argument('--threads', type=int, default=default_threads, help='Number of threads to use. Defaults to current OMP_NUM_THREADS or 1.')parser.add_argument('--reg-only', action='store_true', default=False, help='Only perform initial affine registration.')parser.add_argument('-r', '--reg', metavar='FILE', help='Skip initial affine registration and read transform from file.')parser.add_argument('--init-reg', metavar='FILE', help='Initial affine registration.')parser.add_argument('-a', '--atlas', metavar='DIR', help='Point to an alternative atlas directory.')parser.add_argument('--gmm', metav ar='FILE', help='Point to an alternative GMM file.')parser.add_argument('--ignore-unknown', action='store_true', help='Ignore final priors corresponding to unknown class.')parser.add_argument('--options', metavar='FILE', help='Override advanced options via a json file.')parser.add_argument('--pallidum-separate', action='store_true', default=False, help='Move pallidum outside of global white matter class. Use this flag when T2/flair is used.')# optional lesion optionsparser.add_argument('--lesion', action='store_true', default=False, help='Enable lesion segmentation (requires tensorflow).')parser.add_argument('--threshold', type=float, default=0.3, help='Lesion threshold for final segmentation. Lesion segmentation must be enabled.')parser.add_argument('--samples', type=int, default=50, help='Number of samples for lesion segmentation. Lesion segmentation must be enabled.')parser.add_argument('--burnin', type=int, default=50, help='Number of burn-in samples for lesion segmentation. Les ion segmentation must be enabled.')parser.ad! d_argume nt('--lesion-pseudo-samples', nargs=2, type=float, default=[500, 500], help='Lesion pseudo samples mean and variance.')parser.add_argument('--lesion-rho', type=float, default=50, help='Lesion ratio.')parser.add_argument('--lesion-mask-structure', default='Cortex', help='Intensity mask brain structure. Lesion segmentation must be enabled.')parser.add_argument('--lesion-mask-pattern', type=int, nargs='+', help='Lesion mask list (set value for each input volume): -1 below lesion mask structure mean, +1 above, 0 no mask. Lesion segmentation must be enabled.')# optional debugging optionsparser.add_argument('--history', action='store_true', default=False, help='Save history.')parser.add_argument('--save-posteriors', nargs='*', help='Save posterior volumes to the "posteriors" subdirectory.')parser.add_argument('--save-probabilities', action='store_true', help='Save final modal class probabilities to "probabilities" subdirectory.')parser.add_argument('--showfigs', action='store_true', defaul t=False, help='Show figures during run.')parser.add_argument('--save-mesh', action='store_true', help='Save the final mesh in template space.')parser.add_argument('--save-warp', action='store_true', help='Save the image->template warp field.')parser.add_argument('--movie', action='store_true', default=False, help='Show history as arrow key controlled time sequence.') args = parser.parse_args() # ------ Initial Setup ------ # Make sure freesurfer has been sourcedif not fs.fshome():? ? fs.fatal('FREESURFER_HOME must be set') # Start the process timertimer = fs.utils.Timer() # Create the output folderos.makedirs(args.outputDirectory, exist_ok=True) # Specify the maximum number of threads the GEMS code will usesamseg.setGlobalDefaultNumberOfThreads(args.threads) # Remove previous cost logcostfile = os.path.join(args.outputDirectory, 'cost.txt')if os.path.exists( costfile ):? ? os.remove( costfile )? # Get the atlas directoryatlasDir = os.environ.get('SAMSEG_DATA_DIR')if args.atlas:? ? atlasDir = args.atlasif not atlasDir:? ? # Altas defaults? ? if args.lesion:? ? ? ? defaultAtlas = '20Subjects_smoothing2_down2_smoothingForAffine2_lesion'? ? else:? ? ? ? defaultAtlas = '20Subjects_smoothing2_down2_smoothingForAffine2'? ? atlasDir = os.path.join(fs.fshome(), 'average', 'samseg', defaultAtlas) # Setup the visualization toolvisualizer = samseg.initVisualizer(args.showfigs, args.movie) # ------ Prepare Samseg Parameters ------ # Load user options from a JSON fileuserModelSpecifications = {}userOptimizationOptions = {}if args.options:? ? with open(args.options) as f:? ? ? ? userOptions = json.load(f)? ? if userOptions.get('modelSpecifications') is not None:?? ? ? ? userModelSpecifications = userOptions.get('modelSpecifications')? ? if userOptions.get('optimizationOptions') is not None:?? ? ? ? userOptimizationOptions = userOptions.get('optimizationOptions') # Check if --save-posteriors was specified without any structure search stringif args.save_posteriors is not None and len(args.save_posteriors) == 0:? ? savePosteriors = Trueelse:? ? savePosteriors = args.save_posteriors # ------ Run Samseg ------ samseg_kwargs = dict(? ? imageFileNames=args.inputFileNames,? ? atlasDir=atlasDir,? ? savePath=args.outputDirectory,? ? userModelSpecifications=userModelSpecifications,? ? userOptimizationOptions=userOptimizationOptions,? ? targetIntensity=110,? ? targetSearchStrings=[ 'Cerebral-White-Matter' ],? ? visualizer=visualizer,? ? saveHistory=args.history,? ? saveMesh=args.save_mesh,? ? savePosteriors=savePosteriors,? ? saveWarp=args.save_warp,? ? modeNames=args.mode,? ? pallidumAsWM=(not args.pallidum_separate),? ? saveModelProbabilities=args.save_probabilities,? ? gmmFileName=args.gmm,? ? ignoreUnknownPriors=args.ignore_unknown,) if args.lesion: ? ? # If lesion mask pattern is not specified, assume inputs are T1-contrast? ? lesion_mask_pattern = args.lesion_mask_pattern? ? if lesion_mask_pattern is None:? ? ? ? lesion_mask_pattern = [0] * len(args.inputFileNames)? ? ? ? print('Defaulting lesion mask pattern to %s' % str(lesion_mask_pattern)) ? ? # Delay import until here so that tensorflow doesn't get loaded unless needed? ? from freesurfer.samseg.SamsegLesion import SamsegLesion? ? samseg = SamsegLesion(**samseg_kwargs,? ? ? ? numberOfPseudoSamplesMean=args.lesion_pseudo_samples[0],? ? ? ? numberOfPseudoSamplesVariance=args.lesion_pseudo_samples[1],? ? ? ? rho=args.lesion_rho,? ? ? ? intensityMaskingSearchString=args.lesion_mask_structure,? ? ? ? intensityMaskingPattern=lesion_mask_pattern,? ? ? ? numberOfBurnInSteps=args.burnin,? ? ? ? numberOfSamplingSteps=args.samples,? ? ? ? threshold=args.threshold? ? ) else:? ? samseg = samseg.Samseg(**samseg_kwargs) _, _, _, optimizationSummary = samseg.segment(? ? costfile=costfile,? ? timer=timer,? ? transformFile=args.reg,? ? initTransformFile=args.init_reg,? ? reg_only=args.reg_only) # Save a summary of the optimization processwith open(costfile, 'a') as file:? ? for multiResolutionLevel, item in enumerate(optimizationSummary):? ? ? ? file.write('atlasRegistrationLevel%d %d %f\n' % (multiResolutionLevel, item['numberOfIterations'], item['perVoxelCost'])) timer.mark('run_samseg complete') xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx PS. Repeating the syntax from below. run_samseg --input /home/developer/subjects_new/o_ADNI_002_S_4654__MRI-m072__LMCI-LMCI__20180522__T30-acc_orig__S689126_I1001975.nii /home/developer/subjects_new/rT1_o_ADNI_002_S_4654__MRI-m072__LMCI-LMCI__20180522__T2-FLAIR__S689135_I1001984.nii --pallidum-separate --lesion --lesion-mask-pattern 0 1 --output /home/developer/subjects_new/Lesion-test/ -----Original Message----- From: fsbuild <fsbuild(a)contbay.com> To: freesurfer(a)nmr.mgh.harvard.edu Cc: daedalus39(a)aol.com Sent: Thu, Feb 24, 2022 5:15 pm Subject: Re: [Freesurfer] SAMSEG "lesion" (Illegal instruction) ~ running VM_67 Hello Randy, I think the expectation is for users to run ?samseg? from the command line. ?(The samseg script is a front-end you run with command line options, e.g., ?help, which calls samseg_run that in turn runs the samseg python scripts in the freesurfer python distribution which includes the tensorflow code). I can?t speak to the validity of the command + options causing the crash, but I would look too see if a ?core? file was written in the directory where the command ran that produced the ?Illegal instruction? error and subsequent crash. ?The core file might also be under /var/crash. ?If you have the core file you could name it something unique and try uploading it to?https://secure-web.cisco.com/1_8ugcIT497YTUyY1vRRMjZbWfONaiAbR1P1Zg9-6zN… someone to look at. - R. On Feb 24, 2022, at 11:58, daedalus39(a)aol.com wrote: ????????External Email - Use Caution???????? Following up on yesterday's email: I looked up the help text for SAMSEG on the VM (?run_samseg ?help?).??The flag for --lesion indicates that Tensorflow is required.???? --lesion??????? Enable lesion segmentation (requires tensorflow).?I'm not sure is tensorflow is installed in VM_67, but "which tensorflow" returned nothing.? While my question only reported the ?core dump? and a request to check the syntax, I did ask if the ?lesion? flag was implemented in the VM.?? If it's not installed in VM_67, would you be able to offer some guidance as to where the safest download site is and some suggestions as to how to install it? Sincerely, -Randy -----Original Message----- From: daedalus39(a)aol.com To: freesurfer(a)nmr.mgh.harvard.edu <freesurfer(a)nmr.mgh.harvard.edu> Sent: Wed, Feb 23, 2022 1:19 pm Subject: SAMSEG "lesion" (Illegal instruction) ~ running VM_67 Dear Experts, I am trying to test SAMSEG "lesion" on VM_67 and after I entered: run_samseg --input /home/developer/subjects_new/o_ADNI_002_S_4654__MRI-m072__LMCI-LMCI__20180522__T30-acc_orig__S689126_I1001975.nii /home/developer/subjects_new/rT1_o_ADNI_002_S_4654__MRI-m072__LMCI-LMCI__20180522__T2-FLAIR__S689135_I1001984.nii --pallidum-separate --lesion --lesion-mask-pattern 0 1 --output /home/developer/subjects_new/Lesion-test/ ...I got the following error Illegal instruction (core dumped) Is there anything glaringly wrong in my instruction/input phrase? Is SAMSEG "lesion" implemented in the new VM?? I was able to test the "basic" SAMSEG with a single T1 earlier this morning (it ran just fine) Thanks in advance for any help. -Randy_______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://secure-web.cisco.com/1ajCHs20Ntg5vd9AD9I6GP72nyffMyNANWVvUGOngP_c0a…

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Re: [Freesurfer] Annotation File ROIs to Volume
by Jacoby, John 28 Feb '22

28 Feb '22

Ah yep sorry, I see it. Thank you! Best, John

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Fwd: Gcut error: gcutted brain is much smaller than the mask.
by Begüm Cerrahoğlu 28 Feb '22

28 Feb '22

External Email - Use Caution Dear developers, I am trying to clean up the extra dura left after skullstripping. Watershed parameter does not prove to be much helpful and when I try gcut I get the error below. In the archives I came across this exact problem before, https://secure-web.cisco.com/1JREA1RCtgfPRaolYsneD7S5EwcqlaqoCEQHN3rqgzcSwx… However, there was not an end solution available in the archived email exchange. I am not interested in cerebellum and am okay with cutting the cerebellum out of the brain mask as long as it does not interfere with being able to distinctly separate cortex from cerebellum in the following steps. From skullstripping tutorials, I have read that one should not start erasing cerebellum from the brainmask directly and was wondering if you could let me know why? In sum, are there important reasons to keep the cerebellum despite only being interested in analyzing the cortex? If not, could you please let me know what could be the reason for gcut's failure and if there is anyway to disable failure detection so I can see if the gcutted brain is usable? >> " rm -f brainmask.gcuts.mgz >> mri_gcut -110 -mult brainmask.auto.mgz T1.mgz brainmask.auto.mgz >> brainmask.gcuts.mgz >> >> INFO: Care must be taken to thoroughly inspect your data >> when using mri_gcut. In particular, inspect the edges of >> gm and cerebellum for over-aggressive cutting. >> Add -segmentation brainmask.gcuts.mgz to the tkmedit >> command string to view the voxels which gcut has removed. >> >> reading mask... >> white mean: 107.529232 >> threshold set to: 107.529232*0.400000=43.011693 >> calculating weights... >> doing mincut... >> now doing maxflow, be patient... >> g-cut done! >> post-processing... >> post-processing done! >> masking... >> ** Gcutted brain is much smaller than the mask! >> ** Using the mask as the output instead! >> >> cp brainmask.auto.mgz brainmask.mgz " 1) FreeSurfer version: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0. 2) Platform: Linux Mint 20.2 Thank you greatly for your time and efforts. Kindest regards, Begum Cerrahoglu

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How to make a planar cut in Freeview 7.1.1
by Brandon Ingram 27 Feb '22

27 Feb '22

External Email - Use Caution Hi all, I have been trying to create a flat patch of occipital cortex using the following tutorial (https://secure-web.cisco.com/18Kww5tnkyQOlM1ft0T_n7raXdSOUfLM9sJBa4TZ-zMjq2…) I have tried following the instructions in Freeview and am able to create a cut down the calcarine sulcus, but cannot find the “cut plane” button described. I was wondering whether this is implemented in Freeview, or whether this tool is only available in tksurfer? Freesurfer Version: 7.1.1 OS: Mac OS, Monterey 12.2.1 Many thanks! Brandon

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Re: [Freesurfer] SAMSEG "lesion" (Illegal instruction) ~ running VM_67
by fsbuild 26 Feb '22

26 Feb '22

External Email - Use Caution Hello Randy, I think the expectation is for users to run “samseg” from the command line.  (The samseg script is a front-end you run with command line options, e.g., —help, which calls samseg_run that in turn runs the samseg python scripts in the freesurfer python distribution which includes the tensorflow code). I can’t speak to the validity of the command + options causing the crash, but I would look too see if a “core” file was written in the directory where the command ran that produced the “Illegal instruction” error and subsequent crash.  The core file might also be under /var/crash.  If you have the core file you could name it something unique and try uploading it to https://secure-web.cisco.com/13zdjoSMY5sCPpxW673b6aDxUESbBUC7j-BF_P… someone to look at. - R. On Feb 24, 2022, at 11:58, daedalus39(a)aol.com wrote:        External Email - Use Caution        Following up on yesterday's email:I looked up the help text for SAMSEG on the VM (“run_samseg –help”).  The flag for --lesion indicates that Tensorflow is required.     --lesion        Enable lesion segmentation (requires tensorflow). I'm not sure is tensorflow is installed in VM_67, but "which tensorflow" returned nothing.  While my question only reported the “core dump” and a request to check the syntax, I did ask if the “lesion” flag was implemented in the VM.  If it's not installed in VM_67, would you be able to offer some guidance as to where the safest download site is and some suggestions as to how to install it?Sincerely,-Randy-----Original Message-----From: daedalus39(a)aol.comTo: freesurfer(a)nmr.mgh.harvard.edu <freesurfer(a)nmr.mgh.harvard.edu>Sent: Wed, Feb 23, 2022 1:19 pmSubject: SAMSEG "lesion" (Illegal instruction) ~ running VM_67Dear Experts,I am trying to test SAMSEG "lesion" on VM_67 and after I entered:run_samseg --input /home/developer/subjects_new/o_ADNI_002_S_4654__MRI-m072__LMCI-LMCI__20180522__T30-acc_orig__S689126_I1001975.nii /home/developer/subjects_new/rT1_o_ADNI_002_S_4654__MRI-m072__LMCI-LMCI__20180522__T2-FLAIR__S689135_I1001984.nii --pallidum-separate --lesion --lesion-mask-pattern 0 1 --output /home/developer/subjects_new/Lesion-test/...I got the following errorIllegal instruction (core dumped)Is there anything glaringly wrong in my instruction/input phrase?Is SAMSEG "lesion" implemented in the new VM?  I was able to test the "basic" SAMSEG with a single T1 earlier this morning (it ran just fine)Thanks in advance for any help.-Randy_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Using mri_transform with output of bbregister
by Tisdall, Dylan 25 Feb '22

25 Feb '22

External Email - Use Caution Hi all, Thanks again for all the help so far with getting my data registered and surfaces extracted. I have one further issue that I'm hoping to get help with. I've used bbregister to align my T2 scan with the surfaces from my T1 scan. However, the output is resampled down to 1mm iso and a 256^3 volume; I'd like to keep the native 0.8 mm resolution and FOV if possible (acknowledging, of course, there's actually some blurring in the interpolation, but just for the sake of nominal consistency). I tried to work around this by applying the .lta output by bbregister to my T2 scan (with the goal of eventually using the --out-like flag to specify the sampling resolution, but not doing that yet): mri_transform T2_SPACE.nii.gz T2_SPACE_transform.lta T2_SPACE_warped.nii.gz However, when I load the resulting output volume (T2_SPACE_warped.nii.gz) in freeview, it has swapped axes. Strangely, this isn't the case with the output volume generated by bbregister... it's well-aligned with the surfaces. Similarly, if I load the T2_SPACE.nii.gz into freeview, and apply T2_SPACE_transform.lta as part of the load command, the volume is well-aligned. So what's different about how mri_transform applies that .lta file, compared to bbregister and freeview? Is there a way to just get bbregister to resample my T2 scan with the original resolution and FOV, so I can avoid applying mri_transform altogether? I don't see an --out-like option for bbregister, but is there a different flag? Thanks again, Dylan

2 1

Neverending mris_fix_topology
by Peled, Noam 25 Feb '22

25 Feb '22

Dear group, I'm trying to run recon-all (freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551) on my Martinos' desktop. I killed it after waiting quite a of time for the mris_fix_topology to be completed: Waiting for PID 225967 of (225964 225967) to complete... What can I do to be able to process this subject? I attached the recon-all log. You can also find all the logs here: /autofs/space/mmvtclin_001/thibault/1/users/npeled/subjects/UN07/scripts Thanks! Noam

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PetSurfer: subcortical volume-based analysis
by Jennifer Bramen 25 Feb '22

25 Feb '22

External Email - Use Caution Dear Freesurfer Developers I am doing an ROI--based amyloid PET scan analysis. I have completed all of the steps from the PetSurfer wiki. I now have the preprocessed, averaged, resampled, smoothed PET data in MNI305 space which is constrained to the subcortical gray matter mask. How do I extract mean intensity within all of the subcortical ROI? Thank you! Warm regards, Jennifer Bramen, PhD (she/her/hers) Senior Research Scientist, Neuroimaging Assistant Professor Pacific Brain Health Center | Pacific Neuroscience Institute & Foundation | Providence Saint John's Health Center 1301 20th St. #150 Santa Monica, CA 90404 Phone: 310-525-0865 | Fax: 310-315-4069

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Freesurfer February 2022