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30084 discussions

fspalm contrasts {Disarmed}
by Marina Fernández 23 Dec '20

23 Dec '20

External Email - Use Caution Dear experts, To correct multiple comparisons on the surface I'm using fspalm. I know that this command internally transforms the design contrast and desing matrix from the Freesurfer format to the fsl format so that FSL-PALM understands the input. When the freesurfer contrasts include only one line, I can run permutations with fspalm without errors. The problem arises when the contrast has two lines (e.g., when including a three-level factor like in the example "Contrast 4: group.effect.mtx" from the link https://secure-web.cisco.com/1zRPseSPjbEGgbMXbZRKYmGKkEKOP342L-FeUKM_km6ilB…; or when including a two-way interaction between a dichotomic factor and two covariates of interest). You can see below the error. How can I solve this problem? Thank you in advance. Marina **ERROR:** Loading surface 1/1: /usr/local/freesurfer/subjects/amyloid74_thickness_average/surf/lh.white Reading input 1/1: /usr/local/freesurfer/subjects/amyloid74_thickness_stats/smoothing/gaussians/lh.fsgd_subj_gauss003.mgh Reading design matrix and contrasts. Error using palm_vestread (line 56) File not in the correct format: design.con Error in palm_miscread (line 110) [X.data,X.extra.PPH] = palm_vestread(X.filename); Error in palm_takeargs (line 2111) tmp = palm_miscread(opts.t{t},[],[],opts.precision); Error in palm_core (line 33) [opts,plm] = palm_takeargs(varargin{:}); Error in palm (line 81) palm_core(varargin{:});

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how to use recon-all command
by 1248742467 23 Dec '20

23 Dec '20

External Email - Use Caution Hello, everyone my freesurfer enviroment: Last login: Mon Dec 21 16:45:53 2020 from 10.16.10.109 -------- freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME   /home/tj/application/freesurfer FSFAST_HOME       /home/tj/application/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR      /home/tj/application/freesurfer/subjects cd /home/tj/application/freesurfer/subjects MNI_DIR           /home/tj/application/freesurfer/mni I have a T1.nii.gz file, So where should I put this file in?  What's more, if I want to the output is in the input data file, how to set the recon-all command?

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Can't find Mindboggle datasets
by 1248742467 23 Dec '20

23 Dec '20

External Email - Use Caution Hello, everyone In mindboggle website, the data is freesurfer-output, But I just want to download the 101 source data, use recon -all command preprocess them by myself. I don't know where to download the source datasets, If you know, please give me a link. Thanks Looking forward to your reply

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Converting a binary volume roi.nii file to a label for roi analysis in Freesurfer
by Paul Dhami 23 Dec '20

23 Dec '20

External Email - Use Caution Dear Freesurfer community, I have a volumetric roi.nii file created with spm, based on MNI coordinates from the literature. My goal is to do a roi analysis in Freesurfer, as I am interested in correlating the thickness values of this roi with a behavioral measurer. However, I am lost as to how I can appropriately convert this volumetric roi.nii file to a label. I hate to ask for too much, but can anyone briefly share the commands or steps as to how to convert this roi.nii file to a label so I can conduct an roi analysis within Freesurfer? Thank you very much, Paul

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error in running tkregisterfv
by Peter de Best 23 Dec '20

23 Dec '20

External Email - Use Caution What am I trying to do: I am trying to register my functional resting state scan to the MPRAGE scan (which is saved in the freesurfer subjects directory under ‘subject _30_8_2020’ after running recon-al on a MPRAGE that was aligned to AC PC). The mgz file brain.mgz and the functional scan aligned. What are the commands I use bbregister --s subject_30_8_2020 --mov subject_motion_corrected_func_4D_RestingState.nii --reg affine_TESTTESTTEST6July2337_1_matrix_AVERAGE.dat --init-header –bold tkregisterfv --mov subject_motion_corrected_func_4D_RestingState.nii --reg affine_TESTTESTTEST6July2337_1_matrix_AVERAGEbbb.dat –surfs (bbregister works, tkregisterfv does not; I only provide the bbregistercode for context) What is the error? When I try to run tkregisterfv, I get the following output: “cd /Users/me/Documents/30_8_2020/subject_REST_CF freeview -transform-volume -viewport cor -v /Applications/freesurfer/7.1.1/subjects/subject_30_8_2020/mri/orig.mgz:visible=0:name=orig.mgz(targ) /Users/me/Documents/30_8_2020/subject_REST_CF/subject_motion_corrected_func_4D_RestingState.nii:name=subject_motion_corrected_func_4D_RestingState.nii(mov):reg=/Users/me/Documents/30_8_2020/subject_REST_CF/affine_TESTTESTTEST6July2337_1_matrix_AVERAGEbbb.dat --surface /Applications/freesurfer/7.1.1/subjects/subject_30_8_2020/surf/lh.white:edgecolor=yellow --surface /Applications/freesurfer/7.1.1/subjects/subject_30_8_2020/surf/rh.white:edgecolor=yellow /Applications/freesurfer/7.1.1/bin/fsvglrun: line 20: conditional binary operator expected /Applications/freesurfer/7.1.1/bin/fsvglrun: line 20: syntax error near `FS_ALLOW_VGLRUN' /Applications/freesurfer/7.1.1/bin/fsvglrun: line 20: `if [[ ! -v FS_ALLOW_VGLRUN ]]; then'” My platform: macOS Mojave, version 10.14.6 There is no recon-al log. What I tried to do/ checked: 1) FSL is installed. 2) the fsvglrun text describes fsvgl as a necessary file, and I found that VirtualGL is supposed to contained that, and I tried to install that. It also says that FS_ALLOW_VGLRUN should be set to 1, but I have no idea how to do that. 3) make sure to reboot after every potential solution. None of that worked/ resolved the issue.

2 1

error message when running mri_info
by Jonathan Lynn 23 Dec '20

23 Dec '20

External Email - Use Caution Hello, I've been using a software to process SWI data that includes an option to save the output as nifti files. When I attempt to use either the mri_info or mri_convert commands on these nifti files I receive the following error message: niiRead(): unknown space units 7 in /pfc/common_area/high_pass_1750_1910.nii Where "high_pass_1750_1910.nii" is the name of my nifti file. This leads me to believe there is a problem in how my SWI processing software saves nifti files which makes them incompatible with FreeSurfer. I am curious if it is a problem with some aspect of the nifti header information that is causing me to receive this error and if so, which aspect? Using the fsl program fslhd I have gotten the header info for one of these nifti files and pasted it below: filename high_pass_1750_1910.nii sizeof_hdr 348 data_type INT16 dim0 4 dim1 232 dim2 256 dim3 176 dim4 1 dim5 0 dim6 0 dim7 0 vox_units Unknown time_units rad/s datatype 4 nbyper 2 bitpix 16 pixdim0 0.000000 pixdim1 1.000000 pixdim2 1.000000 pixdim3 1.000000 pixdim4 0.000000 pixdim5 -nan pixdim6 6445431373862396660923732403945472.000000 pixdim7 6445014188069157487771091399081984.000000 vox_offset 352 cal_max 3253932511416847943508928692748288.0000 cal_min 0.0000 scl_slope 0.000000 scl_inter 6444907725225778945067450074398720.000000 phase_dim 0 freq_dim 0 slice_dim 0 slice_name Unknown slice_code -99 slice_start 30622 slice_end -1814 slice_duration 0.000000 time_offset 0.000000 intent Unknown intent_code 73 ´õtent_name ëh`0 intent_p1 0.000000 intent_p2 6444907725225778945067450074398720.000000 intent_p3 68507965883187986432.000000 qform_name Unknown qform_code 0 qto_xyz:1 1.000000 0.000000 0.000000 0.000000 qto_xyz:2 0.000000 1.000000 0.000000 0.000000 qto_xyz:3 0.000000 0.000000 1.000000 0.000000 qto_xyz:4 0.000000 0.000000 0.000000 1.000000 qform_xorient Left-to-Right qform_yorient Posterior-to-Anterior qform_zorient Inferior-to-Superior sform_name Unknown sform_code 0 sto_xyz:1 0.000000 0.000000 0.000000 0.000000 sto_xyz:2 0.000000 0.000000 0.000000 0.000000 sto_xyz:3 0.000000 0.000000 0.000000 0.000000 sto_xyz:4 0.000000 0.000000 0.000000 0.000000 sform_xorient Unknown sform_yorient Unknown sform_zorient Unknown file_type NIFTI-1+ file_code 1 descrip aux_file ¤ô I am hoping someone can help me understand why I am receiving this error from mri_info. Thank you, John

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Extracted mean timecourse from FS label
by Mason Wells 23 Dec '20

23 Dec '20

External Email - Use Caution Hi Experts, I have pre-processed some resting-state date using fMRI prep. I have the functional data on the fs_native surface in bold.func.gii format for each hemisphere. I have created some FS labels and I would like to extract the mean time course from vertices within these labels. Is it possible to use FreeSurfer tools to do this? I have a feeling mri_segstats might be the correct option, but I don't believe this can be used with GIFTI functional data. I tried the command below * mri_segstats --slabel sub-0006 lh /home/masontwells/Documents/freesurfer/subjects/sub-0006/label/lh.wang2015atlas.V1v.label --avgwf out.dat --id 1 --i ../../post-fmriprep/sub-0006_ses-1_task-rest_acq-TR2000_space-fsnative_hemi-L_bold.func.gii However, the terminal produces serval of these messages when the command runs: * ** DA[599] has coordsys with intent NIFTI_INTENT_TIME_SERIES (should be NIFTI_INTENT_POINTSET) I assume this is a sign that the command and data format are not compatible? If this is the case, can you advise on the best way to extract the mean time courses from my functional data? Will I have to resample the volume data to the surface with mri_vol2surf to get it into MGH format and then run mri_segstats? Best wishes, Mason Mason T Wells, MSc PhD student School of Optometry and Vision Sciences & Cardiff University Brain Research Imaging Centre (CUBRIC), School of Psychology Cardiff University Cardiff CF24 4HQ UK Email: WellsMT1(a)cardiff.ac.uk<mailto:WellsMT1@cardiff.ac.uk> Tel: 02920 879628 Web: Cardiff University webpage<https://secure-web.cisco.com/1qzj6G102Hp0-GTfeJ6322xQNXQcW4GkqaH5liYvjrdTN9…><http://secure-web.cisco.com/1wKqfPd1L9yGr-NK1MFwwQm3aX2SenX1VtTlRgPt0wLl12m…> Mason T Wells, MSc Myfyriwr PhD Yr Ysgol Optometreg a Gwyddorau’r Golwg & Canolfan Ymchwil Delweddu’r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol Seicoleg Prifysgol Caerdydd Heol Maindy Caerdydd CF24 4HQ DU E-bost: WellsMT1(a)caerdydd.ac.uk<mailto:WellsMT1@caerdydd.ac.uk> Ffôn: 02920 879628

2 4

Multiple Frames
by Hsieh, Stephanie 23 Dec '20

23 Dec '20

Hi FreeSurfer Developers, I am trying to process a few MPRAGE sequences (different sessions), so I can edit the scans. And I am having trouble reconning the .mgz files. I have looked into why my job terminated early and I have attached the message below. The error states that 'input(s) cannot have multiple frames'. And I then looked into the mri_info, which I have also attached below, and based off of some similar questions I found in the archive, my dimensions seem to be incorrect for freesurfer to process. My dimensions are 240 x 256 x 176 x 2, and I believe they should be 240 x 256 x 176 in order for it to work. How do I go about fixing my dimensions? Does it have to do with how I unpacked the DICOMS? I have not run into this issue before so I would love to learn what caused this error. Thanks in advance, Stephanie Early termination error: Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c INFO: SUBJECTS_DIR is /autofs/cluster/brutha/FS6 Actual FREESURFER_HOME /autofs/cluster/freesurfer/centos6_x86_64/stable6_0_0 Linux compute-0-85.nmr.mgh.harvard.edu<http://compute-0-85.nmr.mgh.harvard.edu/>3.10.0-1160.6.1.el7.x86_64 #1 SMP Tue Nov 17 13:59:11 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux '/autofs/cluster/freesurfer/centos6_x86_64/stable6_0_0/bin/recon-all' -> '/autofs/cluster/brutha/FS6/SCD_021_BL/scripts/recon-all.local-copy' /autofs/cluster/brutha/FS6/SCD_021_BL mri_convert /autofs/cluster/brutha/FS6/SCD_021_BL-1.mgz /autofs/cluster/brutha/FS6/SCD_021_BL/mri/orig/001.mgz mri_convert.bin /autofs/cluster/brutha/FS6/SCD_021_BL-1.mgz /autofs/cluster/brutha/FS6/SCD_021_BL/mri/orig/001.mgz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /autofs/cluster/brutha/FS6/SCD_021_BL-1.mgz... TR=2300.00, TE=2.95, TI=900.00, flip angle=9.00 i_ras = (0.108201, -0.990984, 0.079018) j_ras = (0.0145467, -0.0778978, -0.996855) k_ras = (-0.994023, -0.10901, -0.00598659) writing to /autofs/cluster/brutha/FS6/SCD_021_BL/mri/orig/001.mgz... /autofs/cluster/brutha/FS6/SCD_021_BL mri_convert /autofs/cluster/brutha/FS6/SCD_021_BL-2.mgz /autofs/cluster/brutha/FS6/SCD_021_BL/mri/orig/002.mgz mri_convert.bin /autofs/cluster/brutha/FS6/SCD_021_BL-2.mgz /autofs/cluster/brutha/FS6/SCD_021_BL/mri/orig/002.mgz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /autofs/cluster/brutha/FS6/SCD_021_BL-2.mgz... TR=2300.00, TE=2.95, TI=900.00, flip angle=9.00 i_ras = (0.108201, -0.990984, 0.079018) j_ras = (0.0145467, -0.0778978, -0.996855) k_ras = (-0.994023, -0.10901, -0.00598659) writing to /autofs/cluster/brutha/FS6/SCD_021_BL/mri/orig/002.mgz... #-------------------------------------------- #@# MotionCor Thu Dec 10 21:00:24 EST 2020 Found 2 runs /autofs/cluster/brutha/FS6/SCD_021_BL/mri/orig/001.mgz /autofs/cluster/brutha/FS6/SCD_021_BL/mri/orig/002.mgz Checking for (invalid) multi-frame inputs... ERROR: input(s) cannot have multiple frames! /autofs/cluster/brutha/FS6/SCD_021_BL/mri/orig/001.mgz has 2 frames Linux compute-0-85.nmr.mgh.harvard.edu<http://compute-0-85.nmr.mgh.harvard.edu/>3.10.0-1160.6.1.el7.x86_64 #1 SMP Tue Nov 17 13:59:11 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux recon-all -s SCD_021_BL exited with ERRORS at Thu Dec 10 21:00:25 EST 2020 mri_info on the session I am trying to run: Volume information for SCD_021_BL-1.mgz type: MGH dimensions: 240 x 256 x 176 x 2 voxel sizes: 1.054688, 1.054688, 1.200000 type: SHORT (4) fov: 270.000 dof: 0 xstart: -126.6, xend: 126.6 ystart: -135.0, yend: 135.0 zstart: -105.6, zend: 105.6 TR: 2300.00 msec, TE: 2.95 msec, TI: 900.00 msec, flip angle: 9.00 degrees nframes: 2 PhEncDir: ROW FieldStrength: 3.000000 ras xform present xform info: x_r = 0.1082, y_r = 0.0145, z_r = -0.9940, c_r = 9.2070 : x_a = -0.9910, y_a = -0.0779, z_a = -0.1090, c_a = 36.6058 : x_s = 0.0790, y_s = -0.9969, z_s = -0.0060, c_s = -29.9521 talairach xfm : Orientation : PIL Primary Slice Direction: sagittal voxel to ras transform: 0.1141 0.0153 -1.1928 98.5179 -1.0452 -0.0822 -0.1308 184.0548<tel:184.0548> 0.0833 -1.0514 -0.0072 95.2548 0.0000 0.0000 0.0000 1.0000 voxel-to-ras determinant -1.33484 ras to voxel transform: 0.1026 -0.9396 0.0749 155.6942<tel:155.6942> 0.0138 -0.0739 -0.9452 102.2669<tel:102.2669> -0.8284 -0.0908 -0.0050 98.8026 -0.0000 -0.0000 -0.0000 1.0000 Volume information for SCD_021_BL-2.mgz type: MGH dimensions: 240 x 256 x 176 x 2 voxel sizes: 1.054688, 1.054688, 1.200000 type: SHORT (4) fov: 270.000 dof: 0 xstart: -126.6, xend: 126.6 ystart: -135.0, yend: 135.0 zstart: -105.6, zend: 105.6 TR: 2300.00 msec, TE: 2.95 msec, TI: 900.00 msec, flip angle: 9.00 degrees nframes: 2 PhEncDir: ROW FieldStrength: 3.000000 ras xform present xform info: x_r = 0.1082, y_r = 0.0145, z_r = -0.9940, c_r = 9.2070 : x_a = -0.9910, y_a = -0.0779, z_a = -0.1090, c_a = 36.6058 : x_s = 0.0790, y_s = -0.9969, z_s = -0.0060, c_s = -29.9521 talairach xfm : Orientation : PIL Primary Slice Direction: sagittal voxel to ras transform: 0.1141 0.0153 -1.1928 98.5179 -1.0452 -0.0822 -0.1308 184.0548<tel:184.0548> 0.0833 -1.0514 -0.0072 95.2548 0.0000 0.0000 0.0000 1.0000 voxel-to-ras determinant -1.33484 ras to voxel transform: 0.1026 -0.9396 0.0749 155.6942<tel:155.6942> 0.0138 -0.0739 -0.9452 102.2669<tel:102.2669> -0.8284 -0.0908 -0.0050 98.8026 -0.0000 -0.0000 -0.0000 1.0000

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FREESURFER AND NEURONAVIGATOR IMAGE
by marco.muti＠tin.it 23 Dec '20

23 Dec '20

External Email - Use Caution I need to use freesurfer brain_anat.nii T1 and path.pd.nii (CST WM tract ) in the navigator for neurosurgery. It is necessary to merge the two volume images and to transform it in dicom.Exist a command for that or a procedure in Fressurfer? Or same other software?Thanks!!!!!

2 1

fspalm error : --sig2p-max unknown
by Marina Fernández 23 Dec '20

23 Dec '20

External Email - Use Caution Dear experts, When I was running permutations with fspalm an error appeared because it couldn't find the --sig2p-max option when using mri_surfcluster internally. You can find below the terminal output. How can I fix this error? Thank you in advance Marina. *Terminal output: ... >> >> palm processing complete - running the surface cluster analysis... /usr/local/freesurfer/subjects/merchi182_thickness_stats/stats/thickness/permutation/lctx/across/across_age_cov_none_0.05/pos/lh.fsgd_subj_gauss003/palm mri_surfcluster --in fsp_clustere_tstat_fwep.mgz --thmin 1.301030 --subject merchi182_thickness_average --hemi lh --annot aparc --sum contrast.clustertable.summary --no-fixmni --surf white --ocn contrast.ocn.mgz --oannot ./contrast.ocn.annot --sig2p-max ERROR: Option --sig2p-max unknown error: mri_surfcluster failed fspalm --glmdir /usr/local/freesurfer/subjects/merchi182_thickness_stats//stats/thickness/permutation/lctx/across//across_age_cov_none_0.05/pos//lh.fsgd_subj_gauss003 --cft 1.301 --name palm --iters 100 --cwp .05 --onetail: Signal 127 ans = 255

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