Freesurfer

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30076 discussions

Linear mixed model for longitudinal data
by Julian Macoveanu 09 Mar '22

09 Mar '22

External Email - Use Caution (Apologies for reposting due to lack of answer) Dear all, This is my first attempt to analyze longitudinal structural data with freesurfer, and I just do my best to follow the tutorial. I have some things not clear, so any help would be appreciated. We have a longitudinal study design with 2 groups, healthy and patients who were scanned at baseline a second time following a variable time interval (6 to 36 months). We want to investigate whether the patient’s cortical thickness/volume progresses differently compared to controls (group-by-time interaction effects). I chose to analyze the data with LME due to variable follow-up time, having only 50% of the patients with a second scan, and also having family members within and between groups. Questions 1) To account for familial relationship, should I add a family ID as covariate that stays in the design matrix X and count this covariate as random effect when the model is fitted? Like this: lhstats = lme_mass_fit_Rgw(X,[1 2 3],Y,ni,lhTh0,lhRgs,lhsphere); Where the first 3 covariates in X are counted as random effects: 1 the intercept, 2 follow-up time and 3 family ID. The X would further include group, age, sex, TIV, and group*time, the last one being the interaction term we want to assess using CM.C = [0 0 0 0 0 0 0 1]. Does the X and CM look good to address our research question? 2) It is unclear to me how to perform correction for multiple comparisons and assess what is significant. I follow this procedure after constructing X: [lhTh0,lhRe] = lme_mass_fit_EMinit(X,[1 2 3],Y,ni,lhcortex,3); [lhRgs,lhRgMeans] = lme_mass_RgGrow(lhsphere,lhRe,lhTh0,lhcortex,2,95); lhstats = lme_mass_fit_Rgw(X,[1 2 3],Y,ni,lhTh0,lhRgs,lhsphere); F_lhstats = lme_mass_F(lhstats,CM); dvtx = lme_mass_FDR2(F_lhstats.pval,F_lhstats.sgn,lhcortex,0.05,0): The dvtx is not empty but has 1 value. What I don’t understand, when constructing the sig.mgh map it appears the FDR2 correction info is not used: fs_write_fstats(F_lhstats,mri,'sig.mgh','sig'); How can I be sure when I import sig.mgh in Freeview I only look at the vertexes surviving multiple comparisons? The sig.mgh file shows a lot of regions when thresholded at min 1.3 3) Given a few clusters showing an interaction effect which are saved as sig.mgh and overlaid on surface in freeview, how do I know (visualize) what is going on in these clusters, like which of the group means go up or down over time? (I use FS71 and tksurfer not working). Is it here that printing out and plotting the betas (of the interaction term) are useful for? 4) I have a hypothesis to find differences in prefrontal cortex, at which step would I apply a PFC mask? I have constructed a PFC.label file by adding corresponding label files. Thank you, Julian

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error messages from WSL Freesurfer running the samseg lesion module
by daedalus39＠aol.com 08 Mar '22

08 Mar '22

External Email - Use Caution Dear Experts, Having installed Freesurfer on WSL2, I was able to get the basic FS segmentation to run without error (i.e., recon-all runs just fine). However, when I tried to run_samseg (--lesion) on a pair of T1/co-registered FLAIR images, I received the following error messages Is there anything in the trace (below) that provides a clue? Particularly, I don't understand the "unknown data type ID: 10". Freesurfer accepts NiFTI files My command: run_samseg -o $SUBJECTS_DIR/T1T2-samseg-test -i o_ADNI_002_S_4654__MRI-m072.nii rT1_o_ADNI_002_S_4654__MRI-m072_FLAIR.nii --pallidum-separate --lesion daedalus@DESKTOP-TILLA3B:/usr/local/freesurfer/7-dev/subjects$ run_samseg -o $SUBJECTS_DIR/T1T2-samseg-test -i o_ADNI_002_S_4654__MRI-m072.nii rT1_o_ADNI_002_S_4654__MRI-m072_FLAIR.nii --pallidum-separate --lesion Defaulting lesion mask pattern to [0, 0] 2022-03-08 16:26:09.870925: W tensorflow/stream_executor/platform/default/dso_loader.cc:60] Could not load dynamic library 'libcudart.so.11.0'; dlerror: libcudart.so.11.0: cannot open shared object file: No such file or directory 2022-03-08 16:26:09.870964: I tensorflow/stream_executor/cuda/cudart_stub.cc:29] Ignore above cudart dlerror if you do not have a GPU set up on your machine. WARNING:tensorflow:From /usr/local/freesurfer/7-dev/python/lib/python3.6/site-packages/tensorflow/python/compat/v2_compat.py:96: disable_resource_variables (from tensorflow.python.ops.variable_scope) is deprecated and will be removed in a future version. Instructions for updating: non-resource variables are not supported in the long term ##---------------------------------------------- Samsegment Options ##---------------------------------------------- output directory: /usr/local/freesurfer/7-dev/subjects/T1T2-samseg-test input images: o_ADNI_002_S_4654__MRI-m072.nii, rT1_o_ADNI_002_S_4654__MRI-m072_FLAIR.nii modelSpecifications: {'FreeSurferLabels': [0, 165, 258, ..... This process continues for a few hundred lines and then I see: maximalDeformation=0.0000 minLogLikelihood=-0.8762 appliedScaling: 1.0021 INFO: This is an unsigined short. Traceback (most recent call last): File "/usr/local/freesurfer/7-dev/python/scripts/run_samseg", line 179, in <module> reg_only=args.reg_only File "/usr/local/freesurfer/7-dev/python/packages/freesurfer/samseg/Samseg.py", line 252, in segment initTransform=initTransform File "/usr/local/freesurfer/7-dev/python/packages/freesurfer/samseg/Samseg.py", line 271, in register initTransform=initTransform File "/usr/local/freesurfer/7-dev/python/packages/freesurfer/samseg/Affine.py", line 72, in registerAtlas self.saveResults( savePath, worldToWorldTransformMatrix, imageToImageTransformMatrix ) File "/usr/local/freesurfer/7-dev/python/packages/freesurfer/samseg/Affine.py", line 473, in saveResults inputImage = fs.Volume.read(self.imageFileName) File "/usr/local/freesurfer/7-dev/python/packages/freesurfer/ndarray.py", line 103, in read result = bindings.vol.read(filename) ValueError: unknown MRI data type ID: 10 daedalus@DESKTOP-TILLA3B:/usr/local/freesurfer/7-dev/subjects$

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Hippocampal segmentation Matlab crash
by Caitlin R Bowman 08 Mar '22

08 Mar '22

External Email - Use Caution Hello, I am trying to run the hippocampal segmentation used in freesurfer 7. I have tried with both 7.1.1 and 7.2 and have run into an issue at the same spot. I am running on a computing cluster, not locally. The same code works fine on my local computer. The managers of the computing cluster have tried to help but are stuck themselves. Find the command that I run below followed by the full error log. Best, Cait Command: segmentHA_T2.sh sub-110033 $ANATDIR/sub-110033_T2w.nii.gz T2 0 Error log: ------------------------------ USER bowman2 HOST compute-081.mortimer PROCESSID 11325 PROCESSOR x86_64 OS Linux Linux compute-081.mortimer 3.10.0-1160.49.1.el7.x86_64 #1 SMP Tue Nov 30 15:51:32 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux ------------------------------ #-------------------------------------------- #@# Hippocampal Subfields processing (T2) left Thu Feb 24 14:14:35 CST 2022 ------------------------------------------ Setting up environment variables --- LD_LIBRARY_PATH is .:/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84//runtime/glnxa64:/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84//bin/glnxa64:/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84//sys/os/glnxa64:/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/server:/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/client:/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64:/sharedapps/LS/psych_imaging/fsl/6.0.4/lib:/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84/sys/os/glnxa64::/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84/bin/glnxa64:/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84/runtime/glnxa64:/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/lib/vtk/lib/vtk-5.6/:/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/lib/tcltktixblt/lib/:/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/lib/KWWidgets/lib/KWWidgets:/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/mni/lib:/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/lib ------------------------------------------------------------------------ std::terminate() detected at Thu Feb 24 14:14:37 2022 ------------------------------------------------------------------------ Configuration: Crash Decoding : Disabled Default Encoding : UTF-8 GNU C Library : 2.17 stable MATLAB Architecture: glnxa64 MATLAB Root : /raid-07/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84 MATLAB Version : 8.4.0.150421 (R2014b) Operating System : Linux 3.10.0-1160.49.1.el7.x86_64 #1 SMP Tue Nov 30 15:51:32 UTC 2021 x86_64 Processor ID : x86 Family 6 Model 63 Stepping 2, GenuineIntel Fault Count: 1 Abnormal termination: std::terminate() Register State (captured): RAX = 0000000000000000 RBX = 00002baa657204e8 RCX = 0000000000000000 RDX = 00002baa6570f758 RSP = 00002baa93ffb0b0 RBP = 00002baa93ffb470 RSI = 00002baa654c3fb3 RDI = 00002baa93ffb0c0 R8 = 0000000000000000 R9 = 00002baa60271f90 R10 = 0000000000000000 R11 = 0000000000000000 R12 = 00002baa65730520 R13 = 00002baa93ffc0b0 R14 = 00002baa93ffc090 R15 = 00002baa93ffc470 RIP = 00002baa65422f4e EFL = 0000000000000000 CS = 0000 FS = 0000 GS = 0000 Stack Trace (captured): [ 0] 0x00002baa65422f4e /sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84//bin/glnxa64/libmwfl.so+00966478 _ZN2fl4diag5linux12context_base12capture_dataEv+00000030 [ 1] 0x00002baa65420424 /sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84//bin/glnxa64/libmwfl.so+00955428 [ 2] 0x00002baa740ef0f5 /raid-07/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84/bin/glnxa64/libmwmcr.so+00868597 [ 3] 0x00002baa740f12ca /raid-07/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84/bin/glnxa64/libmwmcr.so+00877258 [ 4] 0x00002baa740f13c1 /raid-07/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84/bin/glnxa64/libmwmcr.so+00877505 [ 5] 0x00002baa740f1743 /raid-07/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84/bin/glnxa64/libmwmcr.so+00878403 [ 6] 0x00002baa740f17b3 /raid-07/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84/bin/glnxa64/libmwmcr.so+00878515 [ 7] 0x00002baa5ffe4a06 /lib64/libstdc++.so.6+00387590 [ 8] 0x00002baa5ffe4a33 /lib64/libstdc++.so.6+00387635 [ 9] 0x00002baa5ffe4c53 /lib64/libstdc++.so.6+00388179 [ 10] 0x00002baa60fe3822 /sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84//bin/glnxa64/libmwi18n.so+00325666 _ZN2fl4i18n14MessageCatalog17GetMessageCatalogERKNS0_9CatalogIDERKNS0_8MwLocaleE+00001186 [ 11] 0x00002baa60fe4113 /sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84//bin/glnxa64/libmwi18n.so+00327955 _ZN2fl4i18n14MessageCatalog11get_messageERKN13resource_core9BaseMsgIDERKNS0_8MwLocaleE+00000051 [ 12] 0x00002baa6589bf57 /sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84//bin/glnxa64/libmx.so+01482583 [ 13] 0x00002baa6589ae6f /sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84//bin/glnxa64/libmx.so+01478255 [ 14] 0x00002baa65832a44 /sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84//bin/glnxa64/libmx.so+01051204 _Z14mxWarningMsgIdRKN13resource_core9BaseMsgIDE+00000052 [ 15] 0x00002baa74443a95 /raid-07/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84/bin/glnxa64/libmwjmi.so+01100437 [ 16] 0x00002baa74443d2f /raid-07/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84/bin/glnxa64/libmwjmi.so+01101103 _Z50mljInitFirstCrackSignalHandlerIfJavaAlreadyStartedv+00000015 [ 17] 0x00002baa740c5855 /raid-07/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84/bin/glnxa64/libmwmcr.so+00698453 [ 18] 0x00002baa740b64ec /raid-07/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84/bin/glnxa64/libmwmcr.so+00636140 [ 19] 0x00002baa740a2cdd /raid-07/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84/bin/glnxa64/libmwmcr.so+00556253 [ 20] 0x00002baa607adea5 /lib64/libpthread.so.0+00032421 [ 21] 0x00002baa60ac0b0d /lib64/libc.so.6+01043213 clone+00000109 If this problem is reproducible, please submit a Service Request via: http://secure-web.cisco.com/1RD2fc7k7E8B1e1GuwRGzMU8V8DVzFuosUwM0pYlETnQWtE… A technical support engineer might contact you with further information. Thank you for your help.** This crash report has been saved to disk as /home/bowman2/matlab_crash_dump.11396-1 ** MATLAB is exiting because of fatal error /sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/bin/run_segmentSubjectT2_autoEstimateAlveusML.sh: line 40: 11396 Killed /sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/bin/segmentSubjectT2_autoEstimateAlveusML sub-CC110037 /home/bowman2/Data/camcan/fs_camcan/ /raid-18/LS/bowman2/camcan/imaging/anat/sub-CC110037/sub-CC110037_T2w.nii.gz 0.333333333333333333333333333333333333 /sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/average/HippoSF/atlas/AtlasMesh.gz /sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/average/HippoSF/atlas/AtlasDump.mgz /sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/average/HippoSF/atlas/compressionLookupTable.txt 0.05 left L-BFGS v21 T2 '/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/bin/fs_run_from_mcr /sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/bin/' 0 1 0 @#@FSTIME 2022:02:24:14:14:35 run_segmentSubjectT2_autoEstimateAlveusML.sh N 18 e 1.65 S 0.13 U 1.19 P 80% M 67608 F 0 R 19447 W 0 c 32 w 559 I 0 O 84720 L 5.00 5.06 4.81 @#@FSLOADPOST 2022:02:24:14:14:37 run_segmentSubjectT2_autoEstimateAlveusML.sh N 18 5.00 5.06 4.81 Linux compute-081.mortimer 3.10.0-1160.49.1.el7.x86_64 #1 SMP Tue Nov 30 15:51:32 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux T2 hippocampal subfields exited with ERRORS at Thu Feb 24 14:14:37 CST 2022 -- Caitlin Bowman, Ph.D. Assistant Professor of Psychology University of Wisconsin-Milwaukee

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Question about editing topology errors
by Trisanna Sprung-Much 08 Mar '22

08 Mar '22

External Email - Use Caution Hi there I have this issue occurring in several hemispheres (See images attached) where a “sulcus” is created because the pial crosses where it shouldn’t, and am wondering what the best way to edit this is. I don’t think it is a matter of adding WM control points as it is not the WM that needs to be corrected but rather the pial. My 2nd image shows how the sulci should look in the pial. Should it be just a matter of removing voxels in the brainmask.mgz and doing recon-all -autorecon-pial -subjid I tried this for one subject and it was not happy. Is there a way to add control points for the pial? Thank you! Trisanna Sprung-Much, PhD McGill University Montreal Neurological Institute --

1 1

Re: [Freesurfer] password for virtual machine
by fsbuild 07 Mar '22

07 Mar '22

External Email - Use Caution Hello Xavier, Sending the into to your email shortly. - R. On Mar 7, 2022, at 17:32, Xavier Caldú Ferrús <xcaldu(a)gmail.com> wrote:        External Email - Use Caution        Dear all,I have just downloaded the virtual machine + ubuntu package and I need the password to log in. Would you be so kind as to send it to me?Thank you very much.Best,Xavier_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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password for virtual machine
by Xavier Caldú Ferrús 07 Mar '22

07 Mar '22

External Email - Use Caution Dear all, I have just downloaded the virtual machine + ubuntu package and I need the password to log in. Would you be so kind as to send it to me? Thank you very much. Best, Xavier

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Co-registration without ant resolution cost
by Salar Dini, Elaheh 07 Mar '22

07 Mar '22

External Email - Use Caution Dear Freesurfer developers, I have a dwi.nii image which I want to co-register on a orig.mgz (produced by running recon-all on the subject's T1 image) file without any drop in the quality of image (i.e. without any resolution cost, or changes in the acquired dwi intensity at each voxel). I was told that if you just translate the image and don't rotate it during co-registration, the quality of the image won't drop, because you don't cut through the existing voxels on the original image in resampling process to fit it in the destination image. Also, I'm not sure if the --no-resample flag in mri_vol2vol helps with that. Can you please guide me toward a better understanding of how co-registration affect the image quality? and ways to prevent that? Freesurfer version: 7.2 & the Platform in use: CentOS7 Thank you and all the best, Ela

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recon-all errors after mri_pretess
by Alexopoulos, Dimitrios 07 Mar '22

07 Mar '22

External Email - Use Caution Hi, we're running FS 7.2 'recon-all -all' on a subject and are getting errors on our cluster (CentOS 8) The attached recon-all.log file is attached for details. The last several lines of the file are below. Any comments as to why its failing? Jim. pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 631 (out of 421942: 0.149547) binarizing input wm segmentation... Ambiguous edge configurations... mri_pretess done @#@FSTIME 2022:03:03:12:51:58 mri_pretess N 4 e 3.84 S 0.01 U 3.70 P 96% M 56636 F 1 R 2214 W 0 c 330 w 325 I 8801 O 646 L 3.37 3.47 3.45 @#@FSLOADPOST 2022:03:03:12:52:02 mri_pretess N 4 3.37 3.47 3.45 #-------------------------------------------- #@# Fill Thu Mar 3 12:52:02 CST 2022 ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

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fcseed with average data
by Marilena Wilding 07 Mar '22

07 Mar '22

External Email - Use Caution Dear FreeSurfers! I'm currently trying to do seed-based analysis. Therefore I'm using fcseed-config and fcseed-sess to configure my seed region. However, since I'm using a dataset that has been preprocessed with fMRIPrep, I'm having a lot of trouble doing this. Although I'm doing surface analyses, it seems that fcseed-sess is deriving the seed time course from the volumetric space (which of course makes sense since aparc+aseg is in volumetric space). I was wondering whether there is any way to use these functions with data, that has already been mapped onto the surface (i.e., fmcpr.sm0.fsaverage.lh)? The fMRIPrep output doesn't produce a template file, that seems to be indispensable for the formation of such a seed region. This is the code I used: fcseed-config -segid 1035 -fcname lh_insula_new.dat -fsd bold -mean -cfg mean.lh_insula_new.config -funcstem fmcpr.sm0.fsaverage.lh (I'm using funcstem since I don't have fmcpr.nii in my folders, only fmcpr.sm0.fsaverage.lh). fcseed-sess -sf sessid -cfg mean.lh_insula_new.config And this is my error: fcseed-sess -sf sessid -cfg mean.lh_insula_1010.config Logfile is /storage/marilena/freesurfer_data/Study_3/Excite_data_3/Project/log/fcseed-sess.lh_insula_1010.dat.log Mon 07 Mar 2022 01:24:38 PM UTC Linux pslg067035.pers.ad.uni-graz.at 5.4.0-100-generic #113-Ubuntu SMP Thu Feb 3 18:43:29 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux setenv SUBJECTS_DIR /storage/marilena/freesurfer_data/Study_3/Excite_data_3/Project/structural/ cd /storage/marilena/freesurfer_data/Study_3/Excite_data_3/Project /usr/local/freesurfer/fsfast/bin/fcseed-sess -sf sessid -cfg mean.lh_insula_1010.config freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b Mon 07 Mar 2022 01:24:38 PM UTC Linux pslg067035.pers.ad.uni-graz.at 5.4.0-100-generic #113-Ubuntu SMP Thu Feb 3 18:43:29 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux setenv SUBJECTS_DIR /storage/marilena/freesurfer_data/Study_3/Excite_data_3/Project/structural/ cd /storage/marilena/freesurfer_data/Study_3/Excite_data_3/Project /usr/local/freesurfer/fsfast/bin/fcseed-sess -sf sessid -cfg mean.lh_insula_1010.config freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b mri_label2vol --seg /storage/marilena/freesurfer_data/Study_3/Excite_data_3/Project/structural//01/mri/aparc+aseg.mgz --reg /storage/marilena/freesurfer_data/Study_3/Excite_data_3/Project/01/bold/001/register.dof6.lta --temp ERROR: could not determine file for /storage/marilena/freesurfer_data/Study_3/Excite_data_3/Project/01/bold/001/template --fillthresh .5 --o /storage/marilena/freesurfer_data/Study_3/Excite_data_3/Project/01/bold/001/tmp.fcseed-sess.470390/seg.nii.gz --pvf /storage/marilena/freesurfer_data/Study_3/Excite_data_3/Project/01/bold/001/tmp.fcseed-sess.470390/pvf.nii.gz ERROR: Option could unknown Thank you a lot in advance!! Best, Marilena

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recon-all permissions problems
by giuseppe messina 06 Mar '22

06 Mar '22

External Email - Use Caution hi i am a neurosurgeon, and i am a newbie in freesurfer, nut i thin i installed it appropriately and the licence txt file is ok i have a macbookpro 16 last generation with 32 gb of memory my freesurfer version is 7.2.0 the problem is that when i run recon-all ( in correct syntax) , permission issues appear; it seems that i dont have permissions to go ahead with the freesurfer. i also used ( as indicated in one of your tutorial ) the sudo chmod -R a+W $SUBJECTS_DIR command, but if i do so, a password is requested in the terminal. really, i dont know hot to solve this problem, please help me Giuseppe Thank you again -- Giuseppe Messina Dept Neurosurgery Istituto Nazionale Neurologico "Carlo Besta", Milan E-mail giusmex(a)gmail.com

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