Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30084 discussions

Infant Freesurfer exiting without error
by COLLEEN PLETCHER 13 May '21

13 May '21

External Email - Use Caution Hi, I am trying to run infant freesurfer using the --segfile and --masked options. When I attempt to run it, it runs for a bit and then I get this: USAGE: mri_or <options> fname1 fname2 .. After this, the program exits. I am not getting any error, so I am confused about why it is exiting suddenly? Thank you very much! -Colleen

2 9

Sulcal probability maps
by Kristi Drudik 12 May '21

12 May '21

External Email - Use Caution Good afternoon, I hope this email finds you well. I am in the process of "painting" MRI surfaces from the Human connectome project in FreeSurfer, meaning creating labels on the surfaces to analyze sulcal morphology. We are interested in the spatial variability of the sulcus and thus, want to create surface spatial probability maps using FreeSurfer (please see attachment for an example of such surface probability maps). These maps would represent the likelihood of each vertex on the FreeSurfer fsaverage surface belonging to the sulcus of interest (from 0% to 100%). To obtain these probability maps, I: * Painted the sulcus of interest on the surface by creating a .label file. * Registered this .label file to fsaverage (mri_label2label) * Converted the .label file to vol (mri_label2vol) * Converted it to a surface file (mri_vol2surf) * Concatenated the data to create an average (mri_concat --mean) * Blurred the data and loaded the blurred average as an overlay onto the fsaverage pial (mris_fwhm) Because this seems very convoluted, my question becomes: Is there a more direct way to generate these maps from the labels themselves, rather than going from label to vol, then back to surf? Finally, I would like these maps to represent a 0-100% range of each vertex in fsaverage belonging to the sulcus of interest. However, this method creates a 0-1 range (please see colour bar in attachment). Is there a way to change this to a percentage? Thank you very much for your time and help. Please let me know if you have any questions. Best, Kristi Kristi Drudik Ph.D. Student, Clinical Psychology Montreal Neurological Institute McGill University Montreal, Canada

3 20

Cluster correction at subject level using -log10(p) values
by Leonardo Tozzi 12 May '21

12 May '21

External Email - Use Caution Dear Experts, I am running an analysis where I have -log10(p) values on the cortical surface of some subjects stored as a MGH file. I would now like to run a cluster level correction on these data at the level of each individual subject using mri_mcsim followed by mri_surfcluster and I would like to constrain my inference to a ROI. I have a few questions. First of all, is it correct that I should to a -log10(p) transform on my p values before entering them in mri_surfcluster? Second, will the csd generated by mcsim be valid to feed in mri_surfcluster since the values are a -log10(p) transformed? Does mcsim -log transform the gaussian noise it uses at some point or is this not necessary? My calls to the two methods are as follows (for one hemisphere): First the mcsim: mri_mcsim --o “${subject}_mcsim_lh_${roi}" --base mc-z --surface ${subject} lh --nreps 10000 --label $roi Then the mri_surfcluster: mri_surfcluster --in "/${subject}_lh_${roi}_neglog10p_signed.mgh" \ --csd "${subject}_mcsim_lh_${roi}/fwhm05/abs/th30/mc-z.csd" \ --clabel "${subject}/label/lh.${roi}.label" \ --cwsig "${subject}_lh_${roi}_neglog10p_abs_clu05.mgh" \ --vwsig "${subject}_lh_${roi}_neglog10p_abs_vox05.mgh" \ --sum "${subject}_lh_${roi}_neglog10p_abs_summary.txt" \ --thmin 3 \ --surf white \ --subject ${subject } \ --hemi lh \ --ocn “${subject}_lh_${roi}_neglog10p_abs_clu05_clunum.mgh" \ --cwpvalthresh 0.05 In the call of mri_surfcluster, I want a cluster forming threshold of p=0.001, which would correspond to -logp(0.001)=3. Is it correct that the argument --thmin should be expressed as -log10(p) but the parameter cwpvalthresh should be p? The reason why I think I did something wrong is that I get a lot of clusters from this analysis, sometimes >15 per individual. This makes me think that the correction might not be as stringent as I would like to. Thank you, Leonardo Tozzi, MD, PhD Williams PanLab | Postdoctoral Researcher Stanford University | 401 Quarry Rd ltozzi(a)stanford.edu<mailto:ltozzi@stanford.edu> | (650) 5615738 Connect with us! [signature_1075933358]<https://secure-web.cisco.com/154LqJFzFLISeYtGLsUgwToWD-mN0G4thIfubhtThzJ6F9…> [signature_1282923475] <http://secure-web.cisco.com/11JA0cps0LSyc_YKkvLkjj53ioS8G144vcOsjQghqMz-F2M…> [signature_911042299] <https://secure-web.cisco.com/1Mkao1uevqs0RL-8o0FG2efSSKGQAOwrHeahbv3dcsTbir…>

2 6

volume ROI to surface for cortical thickness
by M Pope 12 May '21

12 May '21

External Email - Use Caution Dear Freesurfer experts, I have created volumetric ROIs of entorhinal cortex regions and have registered them to subjects’ native space (T1). I now wish to register them to the subject surface in order to get information such as cortical thickness- using mri_vol2surf and mri_segstats I believe. I was looking at your tutorial regarding this VolumeRoiCorticalThickness - Free Surfer Wiki (harvard.edu)<https://secure-web.cisco.com/1NhD55JOKQjBEatrGH8aFF1vX2Pc2cSmUgIdVJu201vnm4…> and had a few questions. First of all- could you explain why you are going through fsaverage. Is there some kind of advantage to doing this procedure of registration, mri_vol2surf and then mri_surf2surf rather than just using mri_vol2surf with the subject space as the regheader?? When I tried through fsaverage as explained in the tutorial (following the exact same commands) the ROI appeared wrong in the surface and the thickness stats were incorrect. Secondly, when doing the procedure as per the tutorial, do you mean that we have to register each subject's mask to the fsaverage- or only one, e.g a ROI derived from the subject-specific group template (we have one produced through ANTs). Lastly- some explanation about how projfrac and projdist work would be very helpful. What numbers are considered best practice? Thankyou, Marianna Pope

2 4

Registering preop and postop MRI scans
by Peled, Noam 11 May '21

11 May '21

Dear group, I have preop and postop MRI scans of an epileptic patient. I ran recon-all on the preop, and bbregister on the postop to register it to the preop. I'm not sure why, but the results weren't really good. Maybe I should try using the longitudinal pipeline? Thanks, Noam

2 2

About segmentation of hippocampal subfields and nuclei of the amygdala
by 笹林大樹 11 May '21

11 May '21

External Email - Use Caution Dear Freesurfer experts, I am trying to assess volumes of hippocampal subfields and amygdala nuclei using Freesurfer (ver7.0). However, after following the URL below and using Matlab R2014b runtime, I am unable to proceed any further with the analysis because Matlab quits in the middle of the runtime due to an error. https://secure-web.cisco.com/1DH7AiF5RJ4wYplilcwV6vMLR0ziT4UWVek6O3a6IVZCy9… <https://secure-web.cisco.com/1DH7AiF5RJ4wYplilcwV6vMLR0ziT4UWVek6O3a6IVZCy9…> I contacted Mathworks and they instructed me to contact someone who is familiar with the operation of FreeSurfer. Therefore, could you please let us know how to solve this problem? I also attached the log. Thank you very much, Daiki Sasabayashi

2 2

Capture multiple images using freeview
by Xiaojiang Yang 11 May '21

11 May '21

External Email - Use Caution Dear FS developers, I know how to use freeview to capture one static image and save it to a file. For example, I can capture coronal view's slice 100 using this command: freeview \ -v $SUBJECTS_DIR/$subjectid/mri/orig.mgz \ -f $SUBJECTS_DIR/$ subjectid /surf/lh.white:edgecolor='255,255,255' \ -f $SUBJECTS_DIR/$ subjectid /surf/lh.pial:edgecolor='0,0,255' \ -f $SUBJECTS_DIR/$ subjectid /surf/rh.white:edgecolor='255,255,255' \ -f $SUBJECTS_DIR/$ subjectid /surf/rh.pial:edgecolor='0,0,255' \ -viewsize 1024 1024 -viewport coronal --nocursor -zoom 1.5 \ -slice 127 127 *100 *-ss tmp/captued My first question is: how can I capture all 256 coronal slices using one freeview command? If I use a loop to run that above freeview command, it would be very very slow, because it needs to load the volume and all surfaces 256 times. Do you have a method that allows me to load the volume and surfaces only once and capture many images and save them? My 2nd question is: do you have a method to capture images in the background without needing to open the freeview GUI? Thanks John

1 0

LGI error on FS7.1
by Zeng, Victor (BIDMC - Keshavan - Psychiatry) 11 May '21

11 May '21

Hi, I am using Matlab R2014a, and FS7.1.0 and receiving this error when I try to run -localGI. Is there a package I might be missing? Or am I using an outdated version of Matlab? ================= mris_smooth -nw -n 30 /mnt/V/Datasets/BSNIP2/Processing/Finished/24015_S5437DFD_ASSET/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer-main ./lh.pial-outer-smoothed ================= smoothing for 30 iterations smoothing surface tessellation for 30 iterations... smoothing complete - recomputing first and second fundamental forms... ================= mris_euler_number ./lh.pial-outer-smoothed ================= euler # = v-e+f = 2g-2: 61554 - 184656 + 123104 = 2 --> 0 holes F =2V-4: 123104 = 123108-4 (0) 2E=3F: 369312 = 369312 (0) total defect index = 0 ================= mris_convert -n lh.pial-outer-smoothed /mnt/V/Datasets/BSNIP2/Processing/Finished/24015_S5437DFD_ASSET/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer-smoothed-normals.asc ================= ================= find_corresponding_center_FSformat('lh.pial','lh.pial-outer-smoothed',100,'/mnt/V/Datasets/BSNIP2/Processing/Finished/24015_S5437DFD_ASSET/surf/tmp-mris_compute_lgi-lh.pial','/tmp/mrc_30700_.m'); exit ================= < M A T L A B (R) > Copyright 1984-2014 The MathWorks, Inc. R2014a (8.3.0.532) 64-bit (glnxa64) February 11, 2014 . . . To get started, type one of these: helpwin, helpdesk, or demo. For product information, visit http://secure-web.cisco.com/19tcoYq0b9VO4ndLxRqJ8z0rI8AoZ3PjjUlX3NMoW1hFDf9…. >> Warning: Input argument must be a string. > In ver at 41 In freesurfer_read_surf at 70 In find_corresponding_center_FSformat at 26 Error using fprintf Function is not defined for 'struct' inputs. Error in freesurfer_read_surf (line 70) fprintf('FREESURFER_READ_SURF [v %s]\n',ver(11:15)); Error in find_corresponding_center_FSformat (line 26) [mesh_pial.vertices, mesh_pial.faces] = freesurfer_read_surf(pial); >> ERROR: find_corresponding_center_FSformat did not complete successfully! Command exited with non-zero status 1 @#@FSTIME 2021:05:11:17:18:12 mris_compute_lgi N 2 e 31.58 S 6.20 U 53.23 P 188% M 1319608 F 0 R 1468406 W 0 c 71733 w 7023 I 8832 O 30496 L 17.98 17.99 18.00 @#@FSLOADPOST 2021:05:11:17:18:44 mris_compute_lgi N 2 17.35 17.83 17.95 Linux Gamma 3.16.0-4-amd64 #1 SMP Debian 3.16.7-ckt25-2+deb8u3 (2016-07-02) x86_64 GNU/Linux recon-all -s 24015_S5437DFD_ASSET exited with ERRORS at Tue May 11 17:18:44 EDT 2021 For more details, see the log file /mnt/V/Datasets/BSNIP2/Processing/Finished/24015_S5437DFD_ASSET/scripts/recon-all.log To report a problem, see http://secure-web.cisco.com/1tb0Ac8lCR6JdEw2vyP10SJNFvPDfcz-cQZjb7S8SDNovcH… Victor Zeng Beth Israel Deaconess Medical Center Keshavan Lab -- ________________________________ This message is intended for the use of the person(s) to whom it may be addressed. It may contain information that is privileged, confidential, or otherwise protected from disclosure under applicable law. If you are not the intended recipient, any dissemination, distribution, copying, or use of this information is prohibited. If you have received this message in error, please permanently delete it and immediately notify the sender. Thank you.

2 1

mri_surf2surf fsaverage to fsaverage_sym
by Mason Wells 11 May '21

11 May '21

External Email - Use Caution Hi experts, I am trying to resample some surface overlays from fsaverage to fsaverage_sym surface. I have used the following command: mri_surf2surf --srcsubject fsaverage --srcsurfreg fsaverage_sym.sphere.reg --trgsubject fsaverage_sym --trgsurfreg sphere.reg --hemi lh --sval lh.wang15_mplbl.mgz --tval lh.wang15_mplbl_fsaverage_sym.mgh However, the data in the overlay has changed. The original overlay contains whole values, whereas the resampled overlay on _sym surface contains decimal numbers also. I wondered if you could advise me on whether the command I am using is appropriate? 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/1CvT3G8RZzzxB6qg-HVyDhPR9VtVV6oy-Fcow5GQgw73yM…><http://secure-web.cisco.com/1v3UGT0WTsmMTaF1Wr-gr63WKQjs1maXxrffA76Jy4Uap_7…> 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 1

Error in SAMSEG preprocessing
by Alberto Del Cerro Leon 11 May '21

11 May '21

External Email - Use Caution Hello, I am trying to use SAMSEG to segment white matter lesions, I ran the following command: run_samseg --input '/home/neuroimage/fsl/vascular/1002/U1002_3DT1.nii' '/home/neuroimage/fsl/vascular/1002/flair_reg.nii' --pallidum-separate --lesion --lesion-mask-pattern 0 1 --output '/home/neuroimage/fsl/vascular/1002/' The output files were: - cost.txt - priors-testing.mgz - samseg.talairach.lta - template.lta - template_coregistered.mgz - template_transforms.mat However I don't find any file with the white matter lesions segmented or a stat file. I would send you the terminal outputs but is too extensive. Would you help me?

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