Freesurfer

freesurfer@nmr.mgh.harvard.edu

12 participants
30081 discussions

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

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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

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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

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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

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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.

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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?

3 4

mri_ribbon does not return the ribbon
by Caspar M. Schwiedrzik 10 May '21

10 May '21

External Email - Use Caution Hi! I am trying to make a ribbon.mgz from a non-human primate surface recon that does not have an aseg. Following this prior discussion: Re: [Freesurfer] ribbon.mgz Without aseg.mgz (mail-archive.com) <https://secure-web.cisco.com/1ak2oe-adeCSsLNqdcSfpPz47btc0Bg4_-64m15yi4A3ar…> I tried mri_ribbon: mri_ribbon ./surf/rh.white ./surf/rh.pial ./mri/orig.mgz rh.ribbon.mgz Attached is the output. It looks like it roughly follows the grey matter, but especially the sulci seem to be filled. Unfortunately, there is no help for mri_ribbon. Any advice on how to proceed? The above mentioned discussion did not lead to a conclusion on how to get a ribbon without aseg. Thank you! Caspar

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Re: [Freesurfer] Subthalamic nucleus volume
by Tanrada Pansuwan 10 May '21

10 May '21

External Email - Use Caution Dear Douglas, I think my previous reply got lost… Could you possibly elaborate more on how this method will only reflect the registration in that area instead of volume? I got this method from freesurfer tutorial on obtaining custom anatomical ROI analysis.And do you have any suggestion on an alternative method to accurately obtain sub thalamic nucleus volume? Note: these were our original messages Message: 9 Date: Mon, 5 Apr 2021 09:54:24 -0400 From: "Douglas N. Greve" <dgreve(a)mgh.harvard.edu<mailto:dgreve@mgh.harvard.edu>> Subject: Re: [Freesurfer] Subthalamic nucleus volume To: freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> Message-ID: <2737d6a7-618b-cd97-b4a2-fe29f4c1ce49(a)mgh.harvard.edu<mailto:2737d6a7-618b-cd97-b4a2-fe29f4c1ce49@mgh.harvard.edu>> Content-Type: text/plain; charset="utf-8" If you want the volume in the native space, then why not just register your volume to mni space, then map the label back to the individual? You could probably do that all with FSL (or SPM). BTW, the "volume" you get is not at all likely to be accurate. It will just reflect the registration in that area. On 3/30/2021 4:28 PM, T. Pansuwan wrote: ????????External Email - Use Caution ????????External Email - Use Caution Dear Freesurfer experts, As part of my project, I would need to have subthalamic nucleus as one of my ROIs in which this is not available by Freesurfer. I found a probabilistic subthalamic nucleus atlas in FSL atlases (in MNI152 space) and thought I would convert this to fsaverage space. I have attempted: mri_label2vol ?reg $FREESURFER_HOME/average/mni152.register.dat ?seg STN-maxprob-thr25-0.5mm.nii.gz ?temp $FREESURFER_HOME/subjects/fsaverage/mri/orig.mgz ?o STN_mni152_in_mni305.nii.gz But the location was much more dorsal than original, 1) I was wondering if there are alternative methods I should try and what could have been the problem? At the end, I hope to obtain individual subject?s subthalamic nucleus volume, 2) I was wondering how to convert volume in fsaverage space to labels in fsaverage space so that I can convert the labels to native space? Thank you so much! Tanrada Pansuwan Best wishes, Tanrada On 15 Apr 2021, at 15:10, freesurfer-request(a)nmr.mgh.harvard.edu<mailto:freesurfer-request@nmr.mgh.harvard.edu> wrote: Send Freesurfer mailing list submissions to freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> To subscribe or unsubscribe via the World Wide Web, visit https://secure-web.cisco.com/1dS-NlFBksiulwBVJ54OgNH06JWJ8AG7AYE-cayHfJPVbT… or, via email, send a message with subject or body 'help' to freesurfer-request(a)nmr.mgh.harvard.edu You can reach the person managing the list at freesurfer-owner(a)nmr.mgh.harvard.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of Freesurfer digest..." Today's Topics: 1. Re: Skull stripping with T2 (Douglas N. Greve) 2. Re: Regarding xhemi comparison of hemispheres of the same subject (Douglas N. Greve) 3. Re: Decompressed problem during reconall (Douglas N. Greve) 4. Re: Freesurfer Digest, Vol 206, Issue 6 (Douglas N. Greve) 5. Re: Surface registration problem (Douglas N. Greve) 6. Re: aparc+aseg to native space issue (Douglas N. Greve) 7. Re: mkcontrast2 typo in 7.1.1 (Douglas N. Greve) 8. Re: mri_segstats to report empty and non-empty segmentation (Douglas N. Greve) 9. Re: Subthalamic nucleus volume (Douglas N. Greve) (Douglas N. Greve) ---------------------------------------------------------------------- Message: 1 Date: Thu, 15 Apr 2021 09:49:23 -0400 From: "Douglas N. Greve" <dgreve(a)mgh.harvard.edu> Subject: Re: [Freesurfer] Skull stripping with T2 To: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <cedcfba5-f488-2cb9-87eb-f8e778e5384d(a)mgh.harvard.edu> Content-Type: text/plain; charset="utf-8" It looks like you are running a T2 through recon-all, which won't work. recon-all only takes T1-weighted. You can run it through samseg, eg, samseg --i T2_age_reg_bias.nii.gz --o samseg You can then binarize the seg.mgz to get everything inside the skull On 4/7/2021 2:17 PM, Rohan Bareja wrote: ????????External Email - Use Caution Hello, I am doing skull stripping with free surfer v6.0, and have tried various watershed cut-offs to do skull stripping on T2 scans. But, it removes a lot of brain portion. Here are my commands: mri_convert /Applications/freesurfer/subjects/patient_20_t2/mri/T2_age_reg_bias.nii.gz /Applications/freesurfer/subjects/patient_20_t2/mri/001.mgz recon-all -s patient_20_t2 -autorecon1 ## to be used only when increasing or decreasing threshold of skull stripping. recon-all -skullstrip -wsthresh 25 -clean-bm -s patient_12_t2 Is there any way that I can improve?upon this and get better results if I am missing something? Thanks, Rohan _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://secure-web.cisco.com/1dS-NlFBksiulwBVJ54OgNH06JWJ8AG7AYE-cayHfJPVbT… -------------- next part -------------- An HTML attachment was scrubbed... URL: http://secure-web.cisco.com/1buww-Gkw45BntB0FRXChWHofo-oEY5E6O1IGH71SypVxzG… ------------------------------ Message: 2 Date: Thu, 15 Apr 2021 09:52:11 -0400 From: "Douglas N. Greve" <dgreve(a)mgh.harvard.edu> Subject: Re: [Freesurfer] Regarding xhemi comparison of hemispheres of the same subject To: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <9da0b8dc-1a16-ba96-42f4-74425e2a62a8(a)mgh.harvard.edu> Content-Type: text/plain; charset="windows-1252" Yes, I think you should be able to do that. It would be something like mris_apply_reg --sval rh.thickness --tval rh-on-lh.thickness.mgz --streg xhemi/surf/lh.fsaverage_sym surf/lh.fsaverage_sym On 4/7/2021 4:55 PM, Ghassemieh, A. (Anna) wrote: ????????External Email - Use Caution Dear all, I'm currently working on comparing left with right hemisphere activation for individual subjects and using version 7.1.1. Since it is on an individual level, we would like to register the left hemisphere of each subject to their mirrored right hemisphere (or vice versa). When looking at the way this is described in the wiki (*MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1jwehsASIBC762pL0oF1j7dMFQmfqKWgW4aTWTDdidVqpu… <https://secure-web.cisco.com/1b80Mej4E9rovgmSCJq2Tz2wDNVe2geAoqeHRggKKORugG…>), we started to wonder the following: It is suggested to register to the symmetrical template for each subject. However, it is unclear to us why this is necessary since there is already a matched registration via the spherical reg file for each subject. Does anyone know if it is possible to use this for the purpose somehow instead? Kind regards! ------------------------------------------------------------------------ /De informatie opgenomen in dit bericht kan vertrouwelijk zijn en is uitsluitend bestemd voor de geadresseerde. Indien u dit bericht onterecht ontvangt, wordt u verzocht de inhoud niet te gebruiken en de afzender direct te informeren door het bericht te retourneren. Het Universitair Medisch Centrum Utrecht is een publiekrechtelijke rechtspersoon in de zin van de W.H.W. (Wet Hoger Onderwijs en Wetenschappelijk Onderzoek) en staat geregistreerd bij de Kamer van Koophandel voor Midden-Nederland onder nr. 30244197. / /Denk s.v.p aan het milieu voor u deze e-mail afdrukt. / ------------------------------------------------------------------------ /This message may contain confidential information and is intended exclusively for the addressee. If you receive this message unintentionally, please do not use the contents but notify the sender immediately by return e-mail. University Medical Center Utrecht is a legal person by public law and is registered at the Chamber of Commerce for Midden-Nederland under no. 30244197. / /Please consider the environment before printing this e-mail. / _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://secure-web.cisco.com/1dS-NlFBksiulwBVJ54OgNH06JWJ8AG7AYE-cayHfJPVbT… -------------- next part -------------- An HTML attachment was scrubbed... URL: http://secure-web.cisco.com/1bSpiPZTaKWluqtBV_mnyPSCUimLeepD1y_Ts99ELeRWM2N… ------------------------------ Message: 3 Date: Thu, 15 Apr 2021 09:53:45 -0400 From: "Douglas N. Greve" <dgreve(a)mgh.harvard.edu> Subject: Re: [Freesurfer] Decompressed problem during reconall To: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <af2c561b-8677-a404-49a0-399ac5741163(a)mgh.harvard.edu> Content-Type: text/plain; charset="utf-8" Can you send the log file of the run using the nifti as input? The file you attached is for? dicom input. On 4/8/2021 8:39 AM, Banu Femir wrote: ????????External Email - Use Caution Dear FreeSurfer Developers, I've a problem that cannot solve for the last week. I am using virtual box, FS7 on my windows. I run reconall for Bert and checked that it is working.I have an MRI scan of sepstic patients that I got via CD, these are DICOM files but does not end with .dcm. When I try to run reconall, for dcm images I got the following error (the longer version is in the attachment) ........ Loading pixel data JPEG compressed, decompressing cd /home/developer/Documents/7.1.0-1/subjects/sepsis2 fsdcmdecompress --i /home/developer/Documents/7.1.0-1/subjects/D_000001/F_000001 --o /tmp/developer.tmp.decompressed.dcm.0oOV4x --jpeg >& /tmp/developer.tmp.decompressed.dcm.0oOV4x.dcmdjpeg.out ERROR: 512, see /tmp/developer.tmp.decompressed.dcm.0oOV4x.dcmdjpeg.out for more details Command exited with non-zero status 1 @#@FSTIME ?2021:04:08:08:29:16 mri_convert N 2 e 1.97 S 1.19 U 0.60 P 91% M 9200 F 2 R 999 W 0 c 174 w 356 I 32240 O 0 L 0.55 0.33 0.41 @#@FSLOADPOST 2021:04:08:08:29:18 mri_convert N 2 0.55 0.33 0.41 Linux developer-VirtualBox 5.3.0-53-generic #47~18.04.1-Ubuntu SMP Thu May 7 13:10:50 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux recon-all -s sepsis2 exited with ERRORS at Thu Apr ?8 08:29:18 EDT 202 I converted files to nii, this time I decided to run reconall on nii images, it took more time but again failed on talairach transform. I tried to run on different shells but ended up with the same problem. Is it related with my MRI data or computer, how can I understand that? Many thanks! Banu _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://secure-web.cisco.com/1dS-NlFBksiulwBVJ54OgNH06JWJ8AG7AYE-cayHfJPVbT… -------------- next part -------------- An HTML attachment was scrubbed... URL: http://secure-web.cisco.com/1PRxHGCJhftGXtfg7Fn8lu6irxByM5aFTXQzlb1_CT0AR4X… ------------------------------ Message: 4 Date: Thu, 15 Apr 2021 09:57:15 -0400 From: "Douglas N. Greve" <dgreve(a)mgh.harvard.edu> Subject: Re: [Freesurfer] Freesurfer Digest, Vol 206, Issue 6 To: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <a56fd629-7aef-0f74-1622-629b3acf070d(a)mgh.harvard.edu> Content-Type: text/plain; charset="windows-1252" What do you get if you run: cd /home/ns-zalewk/Desktop/memorycube/EVOLVE10/TB0029U2/TB0029U2_T2TEST_FREESURFER/mri UpdateNeeded ../surf/autodet.gw.stats.lh.dat brain.finalsurfs.mgz wm.mgz ../surf/lh.orig.premesh On 4/8/2021 5:59 PM, zalewk wrote: ????????External Email - Use Caution Hi Doug, Sorry for the late reply, and thanks for all your help. Attached is the text file of the output. This was testing autorecon-pial, but the bug is the same no matter if it's autorecon2-wm, autorecon3, or any place it hits the "if ( $ud" statement. Best, Kody Run it with -debug as the first option, capture the output, and send it to us. On 4/1/2021 8:29 PM, zalewk wrote: ????????External Email - Use Caution Hi Freesurfer team, My lab recently switched over from FS6 to FS7 and I think I've encountered a bug with recon-all. I'm running subjects stepwise and editing them, running recon-all with the -autorecon2 and -autorecon3 flags initially are no problem, they run fine.? Trying to re-run them or use the -autorecon2-wm, -autorecon-pial etc. flags lead to crashing at certain parts of the program. The error message I get is "if: expression syntax". Digging into the code, it seems to crash when it hits a line of code "if($ud || $ForceUpdate)". The syntax superficially looks right (I don't know tcsh), checking the variables it seems like $ForceUpdate is never set, but removing it from recon-all doesn't fix the problem. It seems the $ud variable is for checking if updates are needed for a set of volumes passed to the program. I don't know why that would be a problematic argument, removing that part seems to fix it, but this also seems like an important variable and I don't know enough about tcsh to understand why it works after removing it. Can one of the folks who wrote the recon-all script help me out? I'm running the commands step-wise as a work-around, but that is much less convenient. Best, ------------------------------------------------------------------------ *From:* freesurfer-bounces(a)nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of freesurfer-request(a)nmr.mgh.harvard.edu <freesurfer-request(a)nmr.mgh.harvard.edu> *Sent:* Tuesday, April 6, 2021 6:41 AM *To:* freesurfer(a)nmr.mgh.harvard.edu <freesurfer(a)nmr.mgh.harvard.edu> *Subject:* Freesurfer Digest, Vol 206, Issue 6 Send Freesurfer mailing list submissions to ??????? freesurfer(a)nmr.mgh.harvard.edu To subscribe or unsubscribe via the World Wide Web, visit *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1dS-NlFBksiulwBVJ54OgNH06JWJ8AG7AYE-cayHfJPVbT… <https://secure-web.cisco.com/12RCdM4nvnTq08RfLMdhWLNUwwCLn6K8WftCJlAbuQ-Iak…> or, via email, send a message with subject or body 'help' to ??????? freesurfer-request(a)nmr.mgh.harvard.edu You can reach the person managing the list at ??????? freesurfer-owner(a)nmr.mgh.harvard.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of Freesurfer digest..." Today's Topics: ?? 1. Freesurfer Website Ports (Swearingen, Hannah) ?? 2. mris_average_surface fails (?????????) ?? 3. Re: 2mm thick image for hippocampal segmentation. (Ramesh Babu) ?? 4. Re: fMRIPrep BOLD Output (Douglas N. Greve) ?? 5. Re: mri_glmfit error (Douglas N. Greve) ?? 6. Re: Regarding recon all (Douglas N. Greve) ?? 7. Re: retaining label ids (Douglas N. Greve) ?? 8. Re: recon-all bug (Douglas N. Greve) ?? 9. Re: mris_label2annot - make all command exiting with errors ????? (Douglas N. Greve) ? 10. Re: recon-all bug (Douglas N. Greve) ? 11. Re: Dicom Tag Problem Reconall (Douglas N. Greve) ? 12. unsubscribe (Coleman, Katherine) ? 13. Re: mri_gtmpvc error Checking tissue type ERROR: ????? CheckSegTissueType() tissue type for seg (Douglas N. Greve) ? 14. Re: Problem with freesurfer measures (Douglas N. Greve) ? 15. Re: Freesurfer Website Ports (Douglas N. Greve) ? 16. Re: mris_average_surface fails (Douglas N. Greve) ? 17. Re: 2mm thick image for hippocampal segmentation. ????? (Douglas N. Greve) ? 18. Freesurfer Versions - Zeros in the Cortex (Daniel Gutstein) ? 19. Re: mri_gtmpvc error Checking tissue type ERROR: ????? CheckSegTissueType() tissue type for seg (Bahar Hazal Yal??nkaya) ---------------------------------------------------------------------- Message: 1 Date: Mon, 5 Apr 2021 15:20:31 -0400 From: "Swearingen, Hannah" <hannah_swearingen1(a)brown.edu> Subject: [Freesurfer] Freesurfer Website Ports To: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <CAG+grQp1wJ8ywX0StrT4VJO38JYtwfxivTNvdH3KwQrhtwiRGw(a)mail.gmail.com> Content-Type: text/plain; charset="utf-8" ??????? External Email - Use Caution Hi, I am setting up an Access Control List for an isolated VLAN in which my center's neuroimaging computing workstations will be connected to our hospital's network for data back-up. We want to be able to connect to Freesurfer's website while connected to the VLAN, and we need to supply which ports the website accesses. I used nmap to scan and see which ports are open, and I found this: PORT??? STATE? SERVICE 21/tcp? open?? ftp 80/tcp? open?? http 443/tcp open?? https Our hospital's IT is unsure if the FTP port can be opened without a security breach, and they are wondering if we will still be able to access the website without the 21/FTP port opened? Can anyone provide me with that information? Thanks, Hannah -- -------------- next part -------------- An HTML attachment was scrubbed... URL: *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* http://secure-web.cisco.com/1Z2jU2bdOvqYN7XRsGwgQUy7elka3gsRzA8s48KcX5Dvo7B… <http://secure-web.cisco.com/1ualyBux61RpzLkGD44CYIQkn2Y4_hevbBxqq3LGrIElMPQ…> ------------------------------ Message: 2 Date: Tue, 6 Apr 2021 19:39:40 +0900 From: ????????? <m-bakhit(a)fmu.ac.jp> Subject: [Freesurfer] mris_average_surface fails To: Freesurfer support list <Freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <D78D558F-CE86-441D-B824-2D90D22E1749(a)fmu.ac.jp> Content-Type: text/plain; charset="us-ascii" ??????? External Email - Use Caution Hi, I am trying to make an average subject but when the process reaches mris_average_surface it fails as seen below. My command was as follow: make_average_subject --out avgsubject --subjects spl_01 spl_02 spl_03 spl_04 spl_05 spl_06 spl_07 spl_08 spl_09 spl_10 Can you please guide me to solve this issue. Thanks Mudathir ########################################### #@# Making average lh.white surface --------------------- Tue Apr? 6 19:23:39 JST 2021 /Applications/freesurfer/subjects/avgsubject mris_make_average_surface -i 7 -o white -sdir-out /Applications/freesurfer/subjects lh white sphere.reg avgsubject spl_01 spl_02 spl_03 spl_04 spl_05 spl_06 spl_07 spl_08 spl_09 spl_10 reading vertex positions from white... --------------------------------------------------- hemi??????????? = lh avg_surf_name?? = white canon_surf_name = sphere.reg out_sname?????? = avgsubject xform?????????? = talairach.xfm --------------------------------------------------- Is a directory Is a directory ERROR: creating directory / ERROR: creating directory /Applications/freesurfer/subjects/avgsubject/surf mris_average_surface failed ERROR: make_average_surface ################################################# ------------------------------ Message: 3 Date: Tue, 6 Apr 2021 17:40:29 +0530 From: Ramesh Babu <mgrameshbabu2013(a)gmail.com> Subject: Re: [Freesurfer] 2mm thick image for hippocampal ??????? segmentation. To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <CAHRhR0BLJv7Du65i1x0DKkUe1Nm_jxcJauUpkBXQ-JrSQ4ybqg(a)mail.gmail.com> Content-Type: text/plain; charset="utf-8" ??????? External Email - Use Caution Dear Eugenio and Philipp, Thank you very much for your suggestions. Could you please give more input on "acquire the T1WI double and average it after coregistration, this increases the SNR". Should aquire twise the same sequence with 1x1x2 voxel dimension? Thanks Ramesh On Fri, 2 Apr, 2021, 9:00 PM Iglesias Gonzalez, Juan E., < JIGLESIASGONZALEZ(a)mgh.harvard.edu> wrote: That all sounds right, thanks a lot Philipp! Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://secure-web.cisco.com/1yAlNRge1To1jCEouu9JnBYJFnIJRo-86GCJ4EIWmAyj8pk… <http://secure-web.cisco.com/1yAlNRge1To1jCEouu9JnBYJFnIJRo-86GCJ4EIWmAyj8pk…> *From: *<freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of "Saemann, Philipp" <saemann(a)psych.mpg.de> *Reply-To: *Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> *Date: *Friday, April 2, 2021 at 03:51 *To: *Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu>, Umesh Rurdrapatna <umeshrs(a)gmail.com> *Subject: *Re: [Freesurfer] 2mm thick image for hippocampal segmentation. *??????? External Email - Use Caution??????? * Hi, I try to answer but Eugenio may also add comments. Several points that are important: - 1.5 Tesla and 1x1x1 mm3 are at the limit of what the algorithm can manage. - Post-aquisition reslicing to a higher resolution does not really increase the information content. Internally the algorithm works at a much higher resolution, anyway. - If possible, switch to 3 Tesla. - If possible and this is a prospective study, add a coronal T2 image and use the bi-channel option. See papers of Iglesias et al. on this. - What you could also do on a 1.5 T is acquire the T1WI double and average it after coregistration, this increases the SNR. - Generally, isometric resolutions are good due to the symmetry, of course. - Also on 1.5 T, you may go bit below 1 mm with good head immobilization, and a longer scanning time. BRAVO in general is a good T1 option. Best, Philipp ------------------------------ *Von:* freesurfer-bounces(a)nmr.mgh.harvard.edu < freesurfer-bounces(a)nmr.mgh.harvard.edu> im Auftrag von Ramesh Babu < mgrameshbabu2013(a)gmail.com> *Gesendet:* Freitag, 2. April 2021 09:29 *An:* Freesurfer support list; Umesh Rurdrapatna *Betreff:* Re: [Freesurfer] 2mm thick image for hippocampal segmentation. *??????? External Email - Use Caution??????? * Dear experts, Sorry for reposting. I am expecting some response from experts, so that I can proceed with confidence. For our project work, we are looking for hippocampal and its subfield volumes. Using GE 1.5T scanner, we tried a 3D BRAVO sequence with 1x1x1 resolution, 256x256x160 dimension with 8* flip angle which produced images with a lot of noise. Then we tried the same sequence with 1x1x2 resolution, and 256x256x80 FOV, which produced a clean image without noise. When we reformatted the images, it produces 0.5x0.5x1 resolution with 512x512x172 dimension. Is this sequence good for hippocampal volume estimation and subfield segmentation (also for whole-brain VBM analysis)? Could you please suggest to me a correct sequence, if need to be changed? Regards Ramesh _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://secure-web.cisco.com/1IXus-BXNwSxxsWt0Hl4GNJkM1JdHvv3SmnEoV0r7QyM62… <https://secure-web.cisco.com/1IXus-BXNwSxxsWt0Hl4GNJkM1JdHvv3SmnEoV0r7QyM62…> -------------- next part -------------- An HTML attachment was scrubbed... URL: *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* http://secure-web.cisco.com/10HAHHMoqfVXbIsnZjC3GPFSeLwPDYpHwJVyM_B0XNdo_CO… <http://secure-web.cisco.com/1SjrP1YUfUhxBUacQJI1EraM1Bf-jVszSGYYAoLX8QpAag3…> ------------------------------ Message: 4 Date: Tue, 6 Apr 2021 09:11:52 -0400 From: "Douglas N. Greve" <dgreve(a)mgh.harvard.edu> Subject: Re: [Freesurfer] fMRIPrep BOLD Output To: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <0b7e2dda-5e83-a588-7aef-1d029775f75c(a)mgh.harvard.edu> Content-Type: text/plain; charset="windows-1252" Did you check that the bold is really in register with the anat? You can do this with tkregisterfv --mov bold_preproc.nii.gz? --s sub-01--reg deleteme.lta --surfs On 3/31/2021 10:49 AM, Karan Desai wrote: ????????External Email - Use Caution Hi FS Forum, I am following up on this post because after using mri_vol2surf to downsample my scans to fsaverage4, I ended up with empty files when viewed in Freeview. This is the command that I ran generally: mri_vol2surf--srcbold_preproc.nii.gz?--outlh.imagename.nii.gz--regheadersub-01--trgsubject fsaverage4 -hemilh I am assuming there are some tags that I may be missing which are leading me to output with empty nii.gz files. The input bold preprocessed files are viewed normally in Freeview, but the output is empty. Thank you in advance. ------------------------------------------------------------------------ *From:* freesurfer-bounces(a)nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Douglas N. Greve <dgreve(a)mgh.harvard.edu> *Sent:* Thursday, March 18, 2021 9:43 PM *To:* freesurfer(a)nmr.mgh.harvard.edu <freesurfer(a)nmr.mgh.harvard.edu> *Subject:* Re: [Freesurfer] fMRIPrep BOLD Output sounds like you need mri_vol2surf (use --projfrac 0.5) On 3/18/2021 11:38 AM, Karan Desai wrote: ????????External Email - Use Caution Hi Freesurfer List, I am running fMRIPrep and getting the first two FS output files (aseg and aparcaseg seen above in the screenshot), but not the actual file I need which is the one where it is resampled to the mesh. I have run fMRIPrep and have those two files except the actual BOLD series resampled to the surface mesh. Is there?a FS command that can be used to do that one step? Best, Karan _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu? <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1dS-NlFBksiulwBVJ54OgNH06JWJ8AG7AYE-cayHfJPVbT… <https://secure-web.cisco.com/12RCdM4nvnTq08RfLMdhWLNUwwCLn6K8WftCJlAbuQ-Iak…> <https://secure-web.cisco.com/1QIaXg-8LQBS_EXFAPAJlIGB2KdZVTHRQGggikNFrtrkec… <https://secure-web.cisco.com/1QIaXg-8LQBS_EXFAPAJlIGB2KdZVTHRQGggikNFrtrkec…>> _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1dS-NlFBksiulwBVJ54OgNH06JWJ8AG7AYE-cayHfJPVbT… <https://secure-web.cisco.com/12RCdM4nvnTq08RfLMdhWLNUwwCLn6K8WftCJlAbuQ-Iak…> -------------- next part -------------- An HTML attachment was scrubbed... URL: *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* http://secure-web.cisco.com/17gfgYGHQjI10PWAANCO2UOKvUlQ8mMkUIdv9P22YegvFHs… <http://secure-web.cisco.com/16Ov9TD7Y4DmSEaTZWud7UxtIEzU9sbh_JbmU0Wd3khDleI…> ------------------------------ Message: 5 Date: Tue, 6 Apr 2021 09:14:36 -0400 From: "Douglas N. Greve" <dgreve(a)mgh.harvard.edu> Subject: Re: [Freesurfer] mri_glmfit error To: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <0f19df0b-fbd4-19ea-3903-28775075232b(a)mgh.harvard.edu> Content-Type: text/plain; charset="utf-8" The format is not correct. It should be Input SubjectID Class You have SubjectID in there twice On 4/1/2021 1:15 AM, Ishi Tandon AIB, Jaipur wrote: ????????External Email - Use Caution Hello FS experts, I attempted to execute? mri_glmfit on my structural?data through the following command - mri_glmfit --y final.lh.mTBI.volume.10.mgh --fsgd FSGD/mild.tbi.fsgd dods -C contrats/HC-mTBI.mtx --surf fsaverage --cortex --glmdir lh.volume.glmdir But it gives me an error (attached below) indicating?a formatting problem in my FSGD file (attached). I have been trying to figure that out for a while. But I am unable to debug it. Could someone please help me resolve it? Thanks for your time. /Regards,/ /Ishi Tandon/ /B.Tech + M.Tech - Cognitive Neuroscience/ /Amity University, Rajasthan/ _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1dS-NlFBksiulwBVJ54OgNH06JWJ8AG7AYE-cayHfJPVbT… <https://secure-web.cisco.com/12RCdM4nvnTq08RfLMdhWLNUwwCLn6K8WftCJlAbuQ-Iak…> -------------- next part -------------- An HTML attachment was scrubbed... URL: *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* http://secure-web.cisco.com/1i2Q8lqt3Ii3y88F6IHme41jowWhnnUnuTuCg87soGG0yU8… <http://secure-web.cisco.com/1Wi9JzHS7gYvN8fT-L92LCPOitIZ35g0ihUQMVHsDjNM43t…> ------------------------------ Message: 6 Date: Tue, 6 Apr 2021 09:15:04 -0400 From: "Douglas N. Greve" <dgreve(a)mgh.harvard.edu> Subject: Re: [Freesurfer] Regarding recon all To: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <0b627188-d0c3-e1ce-1955-d078f696ba1f(a)mgh.harvard.edu> Content-Type: text/plain; charset="utf-8" Include the flag -cw256 with recon-all! On 4/1/2021 1:52 AM, Amar Shukla wrote: ????????External Email - Use Caution Dear Team, Actually I am trying to test my own data in recon all , but i have taken only one subject for recon. It shows me this error. ERROR! FOV=408.000 > 256 Include the flag -cw256 with recon-all! Inspect orig.mgz to ensure the head is fully visible. **************************************** Linux amar-GV62VR-7RF 5.8.0-48-generic #54~20.04.1-Ubuntu SMP Sat Mar 20 13:40:25 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux -- With Regards, Amar Shukla Assistant Professor, M tech AI ANN(2014-2016), Centre Of Information Technology, UPES Contact :+91 897 977 8016 _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1dS-NlFBksiulwBVJ54OgNH06JWJ8AG7AYE-cayHfJPVbT… <https://secure-web.cisco.com/12RCdM4nvnTq08RfLMdhWLNUwwCLn6K8WftCJlAbuQ-Iak…> -------------- next part -------------- An HTML attachment was scrubbed... URL: *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* http://secure-web.cisco.com/13B4VzLAPFYaghtwCB2deAj4ja6cX24D80HYXRyp0AQeGlN… <http://secure-web.cisco.com/1d93VEPtx_BolB2Jp6bqDSM38_ZQbO7yDxpNY4Kq0soCGP8…> ------------------------------ Message: 7 Date: Tue, 6 Apr 2021 09:15:56 -0400 From: "Douglas N. Greve" <dgreve(a)mgh.harvard.edu> Subject: Re: [Freesurfer] retaining label ids To: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <1acc0845-8087-77ec-c427-ffe427378093(a)mgh.harvard.edu> Content-Type: text/plain; charset="utf-8" I don't understand, please elaborate On 4/1/2021 2:00 PM, miracle ozzoude wrote: ????????External Email - Use Caution Hello Experts, I did like to extract wm whilst retaining the label ids. I tried mri_extract_labels but it didn't work. Any help?would be appreciated. Many?thanks, Paul _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1dS-NlFBksiulwBVJ54OgNH06JWJ8AG7AYE-cayHfJPVbT… <https://secure-web.cisco.com/12RCdM4nvnTq08RfLMdhWLNUwwCLn6K8WftCJlAbuQ-Iak…> -------------- next part -------------- An HTML attachment was scrubbed... URL: *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* http://secure-web.cisco.com/10IulEl-mlXOy0GsvZeOruovfdR5l_pzh0SYVxMbA6q2AVR… <http://secure-web.cisco.com/15E1_kArEIZ7Mn_ngzGqYdfFRN5O7r5N0a3FpZ53KtcsqA3…> ------------------------------ Message: 8 Date: Tue, 6 Apr 2021 09:17:12 -0400 From: "Douglas N. Greve" <dgreve(a)mgh.harvard.edu> Subject: Re: [Freesurfer] recon-all bug To: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <ccd97428-0587-d4cc-88fa-e54f632ea16d(a)mgh.harvard.edu> Content-Type: text/plain; charset="windows-1252" Run it with -debug as the first option, capture the output, and send it to us. On 4/1/2021 8:29 PM, zalewk wrote: ????????External Email - Use Caution Hi Freesurfer team, My lab recently switched over from FS6 to FS7 and I think I've encountered a bug with recon-all. I'm running subjects stepwise and editing them, running recon-all with the -autorecon2 and -autorecon3 flags initially are no problem, they run fine.? Trying to re-run them or use the -autorecon2-wm, -autorecon-pial etc. flags lead to crashing at certain parts of the program. The error message I get is "if: expression syntax". Digging into the code, it seems to crash when it hits a line of code "if($ud || $ForceUpdate)". The syntax superficially looks right (I don't know tcsh), checking the variables it seems like $ForceUpdate is never set, but removing it from recon-all doesn't fix the problem. It seems the $ud variable is for checking if updates are needed for a set of volumes passed to the program. I don't know why that would be a problematic argument, removing that part seems to fix it, but this also seems like an important variable and I don't know enough about tcsh to understand why it works after removing it. Can one of the folks who wrote the recon-all script help me out? I'm running the commands step-wise as a work-around, but that is much less convenient. Best, Kody Zalewski _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1dS-NlFBksiulwBVJ54OgNH06JWJ8AG7AYE-cayHfJPVbT… <https://secure-web.cisco.com/12RCdM4nvnTq08RfLMdhWLNUwwCLn6K8WftCJlAbuQ-Iak…> -------------- next part -------------- An HTML attachment was scrubbed... URL: *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* http://secure-web.cisco.com/1G1AFU_tVB7NWL2mj34rT91IHQ8c8ga8kQZHBAqlAeRj7DH… <http://secure-web.cisco.com/1UGdvHOgh6Ht9amQXS-QZ0Uq0pqC65s0csSGSJ6wvo0irVv…> ------------------------------ Message: 9 Date: Tue, 6 Apr 2021 09:18:35 -0400 From: "Douglas N. Greve" <dgreve(a)mgh.harvard.edu> Subject: Re: [Freesurfer] mris_label2annot - make all command exiting ??????? with errors To: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <0a8872e7-1d93-c58a-4973-d8e161500d05(a)mgh.harvard.edu> Content-Type: text/plain; charset="utf-8" The "-make" functionality does not work in V7. We should have disabled that flag On 4/2/2021 3:41 AM, Marion DURTESTE wrote: ????????External Email - Use Caution Dear?FreeSurfer developers, When running*recon-all -make all *after correcting a few errors from the recon-all output, it exits with an error.?This occurs when the mris_label2annot command is called. Loading /Users/mariondurteste/Documents/PhD/FreeSurfer/ReconstructedAfterQC/ToDo/ALA076_1/surf/lh.orig 1 1376057 FG1 2 16711935 FG2 ERROR: lh.FG2.mpm.vpnl.label, n=580, vertex 119494 out of range If we rerun the -make all command a second time it then finishes without errors.?Do you know why this is ? ?? * FREESURFER version:?freesurfer-darwin-macOS-7.1.1-20200811-8b40551 ?? * Platform: macOS BigSur 11.2.2 Thanks for your help ! Marion D _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1dS-NlFBksiulwBVJ54OgNH06JWJ8AG7AYE-cayHfJPVbT… <https://secure-web.cisco.com/12RCdM4nvnTq08RfLMdhWLNUwwCLn6K8WftCJlAbuQ-Iak…> -------------- next part -------------- An HTML attachment was scrubbed... URL: *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* http://secure-web.cisco.com/172KA8Pa4LYywWbhU_vOBf11xUKjhFPWX9-JUKtFmCI37Sn… <http://secure-web.cisco.com/1muKjKRwTqfEjiFFxaRrvF1H-JGD8LLATjLmtc1bpqxHeWz…> ------------------------------ Message: 10 Date: Tue, 6 Apr 2021 09:19:41 -0400 From: "Douglas N. Greve" <dgreve(a)mgh.harvard.edu> Subject: Re: [Freesurfer] recon-all bug To: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <8ac90e23-495c-4067-424d-f7632644fae1(a)mgh.harvard.edu> Content-Type: text/plain; charset="windows-1252" So the problem is that there are spaces in the path? That will probably cause a lot of FS to fail On 4/2/2021 11:30 PM, zalewk wrote: ????????External Email - Use Caution Hi freesurfer team, I've tried running recon-all as mentioned before with the -xf flag under different conditions. As far as I can tell, any line using the UpdateNeeded function. e.g.: "set ud = `UpdateNeeded $thickness $pial $white`" fails with the following if statement because the variable $ud includes paths as strings in it instead of a 0/1 integer. Setting it to a 1 or 0 beforehand also seems to solve the problem. The function UpdateNeeded only seems to return an integer as an exit status, so I'm not sure why there are path strings in it causing it to fail. If I print out the $ud variable before it fails and the result is: "/subjectDirectory/subjectID_FREESURFER/mri mri mri_FREESURFER /subjectDirectory/subjectID_FREESURFER/mri/mri_FREESURFER/stats 1" It returns the exit status of 1 preceded by the path of the subject's mri directory, just "mri", "mri_FREESURFER" and the subject's stats directory (all subjects in this particular study have the suffix "_FREESURFER"). It prints this out these strings no matter the variables as .mgz file names, or number of variables passed to the UpdateNeeded function. I still don't have a clue what would cause this behavior. The UpdateNeeded function seems to work fine and as intended as far as I can tell, so I still don't know why these paths/strings are being added and causing it to crash. Best, Kody Zalewski ???? Message: 3 ???? Date: Fri, 02 Apr 2021 03:49:02 +0200 ???? From: fsbuild <fsbuild(a)contbay.com> ???? Subject: Re: [Freesurfer] recon-all bug ???? To: freesurfer(a)nmr.mgh.harvard.edu ???? Cc: cmacd(a)neurosurgery.washington.edu ???? Message-ID: <1617328142.6066780ef2824(a)trashmail.com> ???? Content-Type: text/plain; charset="utf-8" ???? ??????? External Email - Use Caution ???? Hello Kody, ???? One thing you could try to get more information printed about what ???? is going on is to edit the very first line in the recon-all script ???? to be: ???? #! /bin/tcsh -xf ???? ? instead of ???? #! /bin/tcsh -f ???? Adding the x option will echo each line in the script as it?s run ???? with the variable values expanded, and seeing that output could ???? help with debugging. ???? - R. ???? On Apr 1, 2021, at 20:29, zalewk <zalewk(a)uw.edu> wrote:        External ???? Email - Use Caution        Hi ???? Freesurfer team, My lab recently switched over from FS6 to ???? FS7 and I think I've encountered a bug with recon-all.. I'm ???? running subjects stepwise and editing them, running recon-all with ???? the -autorecon2 and -autorecon3 flags initially are no problem, ???? they run fine.  Trying to re-run them or use the ???? -autorecon2-wm, -autorecon-pial etc. flags lead to crashing at ???? certain parts of the program. The error message I get is "if: ???? expression syntax". Digging into the code, it seems to crash when ???? it hits a line of code "if($ud || $ForceUpdate)". The syntax ???? superficially looks right (I don't know tcsh), checking the ???? variables it seems like $ForceUpdate is never set, but removing it ???? from recon-all doesn't fix the problem.  It seems the ???? $ud variable is for checking if updates are ! ???? ?needed fo ???? ?r a set of volumes passed to the program. I don't know why that ???? would be a problematic argument, removing that part seems to fix ???? it, but this also seems like an important variable and I don't ???? know enough about tcsh to understand why it works after removing ???? it. Can one of the folks who wrote the recon-all script help me ???? out? I'm running the commands step-wise as a work-around, but that ???? is much less convenient. Best, Kody Zalewski_______________________________________________Freesurfer ???? mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer? _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1dS-NlFBksiulwBVJ54OgNH06JWJ8AG7AYE-cayHfJPVbT… <https://secure-web.cisco.com/12RCdM4nvnTq08RfLMdhWLNUwwCLn6K8WftCJlAbuQ-Iak…> -------------- next part -------------- An HTML attachment was scrubbed... URL: *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* http://secure-web.cisco.com/1zfNDJ3gfiwOFqeXDLW0OO7pZlwjGO6Ghszjqk9ic1--zgk… <http://secure-web.cisco.com/1UIOGKTX2O1vRf8V80WGZqo75dB0bWbP4gK1yupN-yT5AD8…> ------------------------------ Message: 11 Date: Tue, 6 Apr 2021 09:22:33 -0400 From: "Douglas N. Greve" <dgreve(a)mgh.harvard.edu> Subject: Re: [Freesurfer] Dicom Tag Problem Reconall To: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <bcd0a4ad-aa63-ba67-79a1-45f74cd4faf0(a)mgh.harvard.edu> Content-Type: text/plain; charset="utf-8" Can you send /tmp/banu.tmp.decompressed.dcm.1TXZUy.dcmdjpeg.out ? If that is not there any more, run it again and send the newly created file On 4/4/2021 3:57 PM, Banu Femir wrote: ????????External Email - Use Caution Dear Freesurfer Developers, I'm trying to analyze a set of MRI data that I got via CD. Dicom files did not have .dcm extension, so I used a program and they turned into a .dcm image. My reconall run for around 2 hours, after I got an error: Counting frames nframes = 481 nslices = 1 ndcmfiles = 481 PE Dir = UNKNOWN (dicom read) Loading pixel data JPEG compressed, decompressing cd /home/banu/usr/local/freesurfer/subjects/sepsis1dicomwritebelow fsdcmdecompress --i /home/banu/Documents/Sepsis/yeni_dicom_write_below/F_000001.dcm --o /tmp/banu.tmp.decompressed.dcm.1TXZUy --jpeg >& /tmp/banu.tmp.decompressed.dcm.1TXZUy.dcmdjpeg.out ERROR: 512, see /tmp/banu.tmp.decompressed.dcm.1TXZUy.dcmdjpeg.out for more details Linux banuf 4.15.0-51-generic #55-Ubuntu SMP Wed May 15 14:27:21 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux Before that, I got many Warnings about imagenumber, tag serial number, seriesnumber, tag, ect. In case you want I can share the whole log file. I am wondering if there was sth wrong with my .dcm format. If yes, how I can solve this problem? It seems like there was sth wrong with tags, but I really cannot solve the problem. Many thanks! Have a nice and healthy week! Banu _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1dS-NlFBksiulwBVJ54OgNH06JWJ8AG7AYE-cayHfJPVbT… <https://secure-web.cisco.com/12RCdM4nvnTq08RfLMdhWLNUwwCLn6K8WftCJlAbuQ-Iak…> -------------- next part -------------- An HTML attachment was scrubbed... URL: *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* http://secure-web.cisco.com/1JDnumCEX9F_9RvM0OJ5kYaWxbhCZ1sWRVMiHrShksTeW0q… <http://secure-web.cisco.com/1QL771HcydpJ6oRFgVIOYOou_iTTlLo5mZQmWc_-uZV_Dq-…> ------------------------------ Message: 12 Date: Tue, 6 Apr 2021 13:22:57 +0000 From: "Coleman, Katherine" <kcoleman0(a)bwh.harvard.edu> Subject: [Freesurfer] unsubscribe To: "Freesurfer(a)nmr.mgh.harvard.edu" <Freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <218EBD99-160A-4937-B1A6-D7EDEF09AA39(a)bwh.harvard.edu> Content-Type: text/plain; charset="us-ascii" Hello, Please remove me from the free surfer forum mailing list. Thank you, Katherine Katherine Coleman, MS Research Assistant II Mood Trajectories and Outcomes Laboratory Department of Psychiatry [cid:image001.jpg@01D6CE33.2A446E30] -------------- next part -------------- An HTML attachment was scrubbed... URL: *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* http://secure-web.cisco.com/1vLnf_RQQGzsSylJvOFv51VReiOtxegyDZt52tAvvVXmr5y… <http://secure-web.cisco.com/1aku1sv4acbnftoy5IQP1P-8rTHDW-fHT0rei2o4PN5T8MO…> -------------- next part -------------- A non-text attachment was scrubbed... Name: image001.jpg Type: image/jpeg Size: 8106 bytes Desc: image001.jpg Url : *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* http://secure-web.cisco.com/10XNDNF-p4lT7iJ96OAnD0sioUra-b8SoJYW_Omf4zq1a6I… <http://secure-web.cisco.com/1ROLW26xEk-vtEW7syh9R26yVouCvI49b2RgSQF8gAdCWnN…> ------------------------------ Message: 13 Date: Tue, 6 Apr 2021 09:25:59 -0400 From: "Douglas N. Greve" <dgreve(a)mgh.harvard.edu> Subject: Re: [Freesurfer] mri_gtmpvc error Checking tissue type ERROR: ??????? CheckSegTissueType() tissue type for seg To: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <014bcfc7-3d2b-0314-24f2-8d7280900b66(a)mgh.harvard.edu> Content-Type: text/plain; charset="utf-8" You will need to create a new color table. This is not hard, but not easy either. First, there should be a color table already there. I'm not sure what that will be like; it might have your segments in it, it might not. It might be easier to run gtmseg with the standard options and look at the color table, then try to replicate it with your segmentation On 4/5/2021 6:43 AM, Bahar Hazal Yal??nkaya wrote: ????????External Email - Use Caution Hello Freesurfer"s Developers, I am trying to follow */PetSurfer/* (*MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1pfG0Y25l06eW-L9Zaho4ChiL8unNbMe2M0UBq1KCbMQVp… <https://secure-web.cisco.com/1w-20YuJbRV4WuZCKwBm5cwzjrDf_VgyVOkZEOk6P7qaWL…> <https://secure-web.cisco.com/1oGyZvXtztP0MX30hKqio2fJStw1wQuIW11p5b1b0CkNwS… <https://secure-web.cisco.com/1oGyZvXtztP0MX30hKqio2fJStw1wQuIW11p5b1b0CkNwS…>>) to apply PVC to Pet images. Default pipeline is working however, whenever i try to use another atlas, Schaefer parcellation,?mri_gtmpvc command I get following error: WARNING: LTAconcat(): inverting LTA 1 to match geometry Replacing 18 Pruning ctab tissue type schema Checking tissue type ERROR: CheckSegTissueType() tissue type for seg 258 Head-ExtraCerebral not set Failed tissue type check I have searched to list several people who have issued similar errors but unfortunately i could not find any solution that works for me. Below you can find commands I used: $ gtmseg --s subject--o gtmseg.mgz --ctx-annotSchaefer2018_400Parcels_7Networks_order.annot 1000 2000 --ctab Schaefer2018_400Parcels_7Networks_order_LUT.txt $ mri_coreg --s subject --mov AbetaPre.nii.gz --reg AbetaPre.reg.lta $ mri_gtmpvc --i AbetaPre.nii.gz --psf 8 --reg AbetaPre.reg.lta --regheader --seg gtmseg.mgz --default-seg-merge --auto-mask PSF .01 --mgx .01 --km-ref 8 47 --o gtmpvc.output Also I checked the run of gtmseg via "*tkmeditfv*" where i can visualise 258 Head-ExtraCerebral, and additionally I checked *gtmseg.ctab *file also 258 Head-ExtraCerebral in the list. I will be happy to hear from you. Kind regards. -- Ph.D. Bahar Hazal Yal??nkaya _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1dS-NlFBksiulwBVJ54OgNH06JWJ8AG7AYE-cayHfJPVbT… <https://secure-web.cisco.com/12RCdM4nvnTq08RfLMdhWLNUwwCLn6K8WftCJlAbuQ-Iak…> -------------- next part -------------- An HTML attachment was scrubbed... URL: *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* http://secure-web.cisco.com/12oG4v5mgLMhMJDX0Ye28-X7GA2VU4wpRYfayOm-bX1Wb9O… <http://secure-web.cisco.com/1MCQVfpyJdQIjFfSGxxXtz26q4vx31RG95w-pJl2nFsXkS5…> ------------------------------ Message: 14 Date: Tue, 6 Apr 2021 09:28:21 -0400 From: "Douglas N. Greve" <dgreve(a)mgh.harvard.edu> Subject: Re: [Freesurfer] Problem with freesurfer measures To: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <bee9db6e-332d-d5d6-fe10-0e8697f03490(a)mgh.harvard.edu> Content-Type: text/plain; charset="utf-8" It is normal that those give different results. I would expect them to be extremely close to each other, so small that the difference does not matter. But if you had to take one, I'd take the output of mris_anatomical_stats On 4/5/2021 11:47 AM, Alberto Del Cerro Leon wrote: ????????External Email - Use Caution To obtain de stats from mri_anatomical stats i used />>mris_anatomical_stats -a /usr/local/freesurfer/subjects/218/label/rh.myAAL.annot -f///usr/local/freesurfer/subjects/218/stats/rh.myAAL.stats -b 218 rh/ In another hand, the workflow to obatian?the stats from mri_segstats was: /mri_aparc2aseg --s 218 --labelwm --hypo-as-wm --rip-unknown --volmask --o /usr/local/freesurfer/subjects/218/mri/wmmyAAL.mgz //--annot myAAL/ />>//mri_segstats --seg /usr/local/freesurfer/subjects/218/mri/wmmyAAL.mgz//--ctab /home/neuroimage/fsl/FreeSurfer/wmAALColorLUT.txt --sum /usr/local/freesurfer/subjects/218/stats/wmmyAAL.stats / /-//-pv /usr/local/freesurfer/subjects/218/mri/norm.mgz --excludeid 0 --brainmask /usr/local/freesurfer/subjects/218/mri/brainmask.mgz --in /usr/local/freesurfer/subjects/218/mri/norm.mgz/ /--in-intensity-name norm --in-intensity-units MR --subject 218 --surf-wm-vol --etiv/ El lun, 5 abr 2021 a las 15:50, Douglas N. Greve (<dgreve(a)mgh.harvard.edu <mailto:dgreve@mgh.harvard.edu <mailto:dgreve@mgh.harvard.edu>>>) escribi?: ???? What are your command lines? ???? On 3/30/2021 5:24 AM, Alberto Del Cerro Leon wrote: ???? ????????External Email - Use Caution ???? Thanks a lot, It works!, now I have obtained values to ctx and wm ???? volumes for each area. However when I look at the gray matter ???? volume values calculated by mri_anatomical stats, the results are ???? pretty similar to the ctx-ROIs calculated by mri_segstats, but ???? not the same. It is normal? In that case what measure will be ???? more suitable? ???? El lun, 29 mar 2021 a las 5:22, Douglas N. Greve ???? (<dgreve(a)mgh.harvard.edu <mailto:dgreve@mgh.harvard.edu <mailto:dgreve@mgh.harvard.edu>>>) escribi?: ???????? You'll need to create your own color table by adding 3000 to ???????? the left hemi structures and 4000 to the right hemi ???????? structures. Look at the 3000s and 4000s in ???????? $FREESURFER_HOME/FreeSurferColorLUT.txt ???????? On 3/26/2021 10:09 AM, Alberto Del Cerro Leon wrote: ???????? ????????External Email - Use Caution ???????? Hello Douglas, i tried but when i look at the wmparc.mgz ???????? created by the code >>mri_aparc2aseg --s 215 --labelwm ???????? --hypo-as-wm --rip-unknown --volmask --o mri/wmparc.mgz ???????? --annot myAAL it takes the index and the names from ???????? FreeSurferColorLUT instead of the names in the colorLUT ???????? associated?with myAAL.annot then the ROIs are disorganized. ???????? Could you help me with this problem? ???????? El jue, 25 mar 2021 a las 14:59, Douglas N. Greve ???????? (<dgreve(a)mgh.harvard.edu <mailto:dgreve@mgh.harvard.edu <mailto:dgreve@mgh.harvard.edu>>>) ???????? escribi?: ???????????? Look in recon-all.log to find the command that creates ???????????? the wmparc.mgz. Run that command changing the aparc ???????????? annot to your annot and the output to a new file name. ???????????? Look in wmparc.stats; at the top will be an mri_segstats ???????????? command line. Copy that command line changing the file ???????????? names as needed. ???????????? On 3/22/2021 9:06 AM, Alberto Del Cerro Leon wrote: ???????????? ????????External Email - Use Caution ???????????? Thanks!, how can I obtain the white matter volume stats ???????????? using my annotation file? ???????????? El mar, 16 mar 2021 a las 16:59, Douglas N. Greve ???????????? (<dgreve(a)mgh.harvard.edu ???????????? <mailto:dgreve@mgh.harvard.edu <mailto:dgreve@mgh.harvard.edu>>>) escribi?: ???????????????? I think they will give very similar results, but my ???????????????? guess is that #1 is a little better ???????????????? On 3/8/2021 11:40 AM, Alberto Del Cerro Leon wrote: ???????????????? ????????External Email - Use Caution ???????????????? I want to use the annotation file created by ???????????????? myself in fsaverage to calculate the anatomical ???????????????? stats, but i dont?know what is the best workflow. ???????????????? 1. Convert the annotation file to each subject ???????????????? space using mri_sur2surf and using ???????????????? mri_anatomical_stats in each subject ???????????????? 2. Convert the surface of each subject to ???????????????? fsaverage space and use mri_segstats to obtain the ???????????????? data, in this case i dont?know what surface i have ???????????????? to convert to fsaverage space to do it (i can see ???????????????? thickness (lh/rh.thickness) and volume ???????????????? (lh/rh.volume) but not folding index and white ???????????????? matter volume) ???????????????? Any idea? ???????????????? El lun, 8 mar 2021 a las 16:04, Fischl, Bruce (<BFISCHL(a)mgh.harvard.edu ???????????????? <mailto:BFISCHL@mgh.harvard.edu <mailto:BFISCHL@mgh.harvard.edu>>>) escribi?: ???????????????????? Hi Alberto ????????????????????? 1. And 4. Are not properties of single ???????????????????????? surfaces ? they are computed from the ???????????????????????? white and the pial. For 2 and 3 that is ???????????????????????? really up to you ???????????????????? Cheers ???????????????????? Bruce ???????????????????? *From:* freesurfer-bounces(a)nmr.mgh.harvard.edu ???????????????????? <mailto:freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>> <freesurfer-bounces(a)nmr.mgh.harvard.edu ???????????????????? <mailto:freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>>> ???????????????????? *On Behalf Of *Alberto Del Cerro Leon ???????????????????? *Sent:* Monday, March 8, 2021 7:02 AM ???????????????????? *To:* Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu ???????????????????? <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>>> ???????????????????? *Subject:* [Freesurfer] Problem with ???????????????????? freesurfer measures ???????????????????? *????????External Email - Use Caution * ???????????????????? Hello Freesurfer team, I am using an ???????????????????? annotation file that i've created previously ???????????????????? to obtain the measures of some ROIs. To do ???????????????????? that i am using de commands mri_surf2surf and ???????????????????? mri_segstats. I want to obtain the following ???????????????????? measures: ???????????????????? 1. Gray and White Matter Volume ???????????????????? 2. Folding Index ???????????????????? 3. Curvature measures ???????????????????? 4. Thickness ???????????????????? However I don't know what surface in the surf ???????????????????? folder of each subject I have to use. Could u ???????????????????? help me? _______________________________________________ ???????????????????? Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu ???????????????????? <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> ???????????????????? *MailScanner has detected a possible fraud ???????????????????? attempt from "secure-web.cisco.com" claiming ???????????????????? to be* *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1dS-NlFBksiulwBVJ54OgNH06JWJ8AG7AYE-cayHfJPVbT… <https://secure-web.cisco.com/12RCdM4nvnTq08RfLMdhWLNUwwCLn6K8WftCJlAbuQ-Iak…> ???????????????????? <https://secure-web.cisco.com/1YJFf9_v-FCEIEML34ObuC19lwndNnPr3qXQ27W-KJa3aD… <https://secure-web.cisco.com/1YJFf9_v-FCEIEML34ObuC19lwndNnPr3qXQ27W-KJa3aD…>> _______________________________________________ ???????????????? 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"secure-web.cisco.com" claiming to be* *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1dS-NlFBksiulwBVJ54OgNH06JWJ8AG7AYE-cayHfJPVbT… <https://secure-web.cisco.com/12RCdM4nvnTq08RfLMdhWLNUwwCLn6K8WftCJlAbuQ-Iak…> ???? <https://secure-web.cisco.com/1xoPMQAneRNhi_EotQOagMUtvb1b6JAtMOD6p63fHLkJfc… <https://secure-web.cisco.com/1xoPMQAneRNhi_EotQOagMUtvb1b6JAtMOD6p63fHLkJfc…>> _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1dS-NlFBksiulwBVJ54OgNH06JWJ8AG7AYE-cayHfJPVbT… <https://secure-web.cisco.com/12RCdM4nvnTq08RfLMdhWLNUwwCLn6K8WftCJlAbuQ-Iak…> -------------- next part -------------- An HTML attachment was scrubbed... URL: *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* http://secure-web.cisco.com/1CFFW_3B3Myx_aAJOu8HSOzRVYUMoruIBTXb9op5gzwqTlH… <http://secure-web.cisco.com/10rdgbSFv1652RVTOzqLv5B5B-pLOoHK6b76hquUFu6J9qW…> ------------------------------ Message: 15 Date: Tue, 6 Apr 2021 09:29:20 -0400 From: "Douglas N. Greve" <dgreve(a)mgh.harvard.edu> Subject: Re: [Freesurfer] Freesurfer Website Ports To: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <1d438758-e598-6101-209b-5b14bd1ec83a(a)mgh.harvard.edu> Content-Type: text/plain; charset="utf-8" why do you need to connect to the web site? that is not needed to run FS On 4/5/2021 3:20 PM, Swearingen, Hannah wrote: ????????External Email - Use Caution Hi, I am setting up an Access Control List for an isolated VLAN in which my center's neuroimaging computing workstations will be connected to our hospital's network for data back-up. We want to be able to connect to Freesurfer's?website while connected to the VLAN, and we need to supply which ports the website accesses. I used nmap to scan and see which ports are open, and I found this: PORT ? STATE? SERVICE 21/tcp open ? ftp 80/tcp open ? http 443/tcp open ? https Our hospital's IT is unsure if the FTP port can be opened without a security breach, and they are wondering?if we will still be able to access the website without the 21/FTP port opened? Can anyone provide me with that information? Thanks, Hannah -- _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1dS-NlFBksiulwBVJ54OgNH06JWJ8AG7AYE-cayHfJPVbT… <https://secure-web.cisco.com/12RCdM4nvnTq08RfLMdhWLNUwwCLn6K8WftCJlAbuQ-Iak…> -------------- next part -------------- An HTML attachment was scrubbed... URL: *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* http://secure-web.cisco.com/1WeN4tlbzAsBfwrjWq7FJfrFSqdDoCjosWcAZ7u8J2VbLMC… <http://secure-web.cisco.com/1v80tbb4hkKWYcBqxlH8IM1H60RTr3x1pF9tWfV6koHjcRS…> ------------------------------ Message: 16 Date: Tue, 6 Apr 2021 09:30:17 -0400 From: "Douglas N. Greve" <dgreve(a)mgh.harvard.edu> Subject: Re: [Freesurfer] mris_average_surface fails To: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <a6bc5f6a-0e93-3d9b-3070-2d16d56f648e(a)mgh.harvard.edu> Content-Type: text/plain; charset=utf-8; format=flowed Do you have write permissions to /Applications/freesurfer/subjects Of not on a mac On 4/6/2021 6:39 AM, ????????? wrote: ????????? External Email - Use Caution Hi, I am trying to make an average subject but when the process reaches mris_average_surface it fails as seen below. My command was as follow: make_average_subject --out avgsubject --subjects spl_01 spl_02 spl_03 spl_04 spl_05 spl_06 spl_07 spl_08 spl_09 spl_10 Can you please guide me to solve this issue. Thanks Mudathir ########################################### #@# Making average lh.white surface --------------------- Tue Apr? 6 19:23:39 JST 2021 /Applications/freesurfer/subjects/avgsubject mris_make_average_surface -i 7 -o white -sdir-out /Applications/freesurfer/subjects lh white sphere.reg avgsubject spl_01 spl_02 spl_03 spl_04 spl_05 spl_06 spl_07 spl_08 spl_09 spl_10 reading vertex positions from white... --------------------------------------------------- hemi??????????? = lh avg_surf_name?? = white canon_surf_name = sphere.reg out_sname?????? = avgsubject xform?????????? = talairach.xfm --------------------------------------------------- Is a directory Is a directory ERROR: creating directory / ERROR: creating directory /Applications/freesurfer/subjects/avgsubject/surf mris_average_surface failed ERROR: make_average_surface ################################################# _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1dS-NlFBksiulwBVJ54OgNH06JWJ8AG7AYE-cayHfJPVbT… <https://secure-web.cisco.com/12RCdM4nvnTq08RfLMdhWLNUwwCLn6K8WftCJlAbuQ-Iak…> ------------------------------ Message: 17 Date: Tue, 6 Apr 2021 09:33:30 -0400 From: "Douglas N. Greve" <dgreve(a)mgh.harvard.edu> Subject: Re: [Freesurfer] 2mm thick image for hippocampal ??????? segmentation. To: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <715750d4-45f9-180c-d2ae-e0a485e61ffc(a)mgh.harvard.edu> Content-Type: text/plain; charset="utf-8" Twice the same image at 1x1x1, then use mri_robust_template to register and average them together On 4/6/2021 8:10 AM, Ramesh Babu wrote: ????????External Email - Use Caution Dear Eugenio and Philipp, Thank you very much for your suggestions. Could you please give more input on "acquire the T1WI double and average it after coregistration, this increases the SNR". Should aquire twise the same sequence with 1x1x2 voxel dimension? Thanks Ramesh On Fri, 2 Apr, 2021, 9:00 PM Iglesias Gonzalez, Juan E., <JIGLESIASGONZALEZ(a)mgh.harvard.edu <mailto:JIGLESIASGONZALEZ@mgh.harvard.edu <mailto:JIGLESIASGONZALEZ@mgh.harvard.edu>>> wrote: ???? That all sounds right, thanks a lot Philipp! ???? Juan Eugenio Iglesias ???? Senior research fellow ???? CMIC (UCL), MGH (HMS) and CSAIL (MIT) ???? *MailScanner has detected a possible fraud attempt from ???? "secure-web.cisco.com" claiming to be* *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* http://secure-web.cisco.com/18wORKCclp97RoaDR4W5bjLm01wxL2MMPzMGPbzOHy9MBnK… <http://secure-web.cisco.com/1mdpCol0AWkIYzNxEeBAawhC291hHTGqPM7FETd-BgV8E59…> ???? <http://secure-web.cisco.com/1yAlNRge1To1jCEouu9JnBYJFnIJRo-86GCJ4EIWmAyj8pk… <http://secure-web.cisco.com/1yAlNRge1To1jCEouu9JnBYJFnIJRo-86GCJ4EIWmAyj8pk…>> ???? *From: *<freesurfer-bounces(a)nmr.mgh.harvard.edu ???? <mailto:freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>>> on behalf of ???? "Saemann, Philipp" <saemann(a)psych.mpg.de ???? <mailto:saemann@psych.mpg.de <mailto:saemann@psych.mpg.de>>> ???? *Reply-To: *Freesurfer support list ???? <freesurfer(a)nmr.mgh.harvard.edu ???? <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>>> ???? *Date: *Friday, April 2, 2021 at 03:51 ???? *To: *Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu ???? <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>>>, Umesh Rurdrapatna ???? <umeshrs(a)gmail.com <mailto:umeshrs@gmail.com <mailto:umeshrs@gmail.com>>> ???? *Subject: *Re: [Freesurfer] 2mm thick image for hippocampal ???? segmentation. ???? *????????External Email - Use Caution * ???? Hi, ???? I try to answer but Eugenio may also add comments. Several points ???? that are important: ???? -?1.5 Tesla and 1x1x1 mm3 are at the limit of what the algorithm ???? can manage. ???? - Post-aquisition reslicing to a higher resolution does not really ???? increase the information content. Internally the algorithm works ???? at a much higher resolution, anyway. ???? - If possible, switch to 3 Tesla. ???? - If possible and this is a prospective study, add a coronal T2 ???? image and use the bi-channel option. See papers of Iglesias et al. ???? on this. ???? - What you could also?do on a?1.5 T is acquire the T1WI double and ???? average it after coregistration, this increases the SNR. ???? - Generally, isometric resolutions are good due to the symmetry, ???? of course. ???? - Also on 1.5 T, you may go bit below 1 mm with good head ???? immobilization, and a longer scanning time. BRAVO in general is a ???? good T1 option. ???? Best, ???? Philipp ------------------------------------------------------------------------ ???? *Von:*freesurfer-bounces@nmr.mgh.harvard.edu ???? <mailto:freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>> ???? <freesurfer-bounces(a)nmr.mgh.harvard.edu ???? <mailto:freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>>> im Auftrag von ???? Ramesh Babu <mgrameshbabu2013(a)gmail.com ???? <mailto:mgrameshbabu2013@gmail.com <mailto:mgrameshbabu2013@gmail.com>>> ???? *Gesendet:* Freitag, 2. April 2021 09:29 ???? *An:* Freesurfer support list; Umesh Rurdrapatna ???? *Betreff:* Re: [Freesurfer] 2mm thick image for hippocampal ???? segmentation. ???? *????????External Email - Use Caution * ???? Dear experts, ???? Sorry for reposting. I am expecting some response from experts, so ???? that I can proceed with confidence. ???? For our project work, we are looking for hippocampal??and its ???? subfield?volumes. Using GE 1.5T scanner, we?tried a 3D BRAVO ???? sequence with 1x1x1 resolution, 256x256x160 dimension with 8* flip ???? angle which produced images with a lot of noise. Then we tried the ???? same sequence?with 1x1x2 resolution, and 256x256x80 FOV, which ???? produced a clean image without?noise. When we reformatted?the ???? images, it produces 0.5x0.5x1 resolution with 512x512x172 dimension. ???? Is this sequence good for hippocampal volume estimation and ???? subfield segmentation (also for whole-brain VBM analysis)? ???? Could you please suggest to me a correct sequence, if need to be ???? changed? ???? Regards ???? Ramesh ???? _______________________________________________ ???? Freesurfer mailing list ???? Freesurfer(a)nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> ???? *MailScanner has detected a possible fraud attempt from ???? "secure-web.cisco.com" claiming to be* *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1dS-NlFBksiulwBVJ54OgNH06JWJ8AG7AYE-cayHfJPVbT… <https://secure-web.cisco.com/12RCdM4nvnTq08RfLMdhWLNUwwCLn6K8WftCJlAbuQ-Iak…> ???? <https://secure-web.cisco.com/1IXus-BXNwSxxsWt0Hl4GNJkM1JdHvv3SmnEoV0r7QyM62… <https://secure-web.cisco.com/1IXus-BXNwSxxsWt0Hl4GNJkM1JdHvv3SmnEoV0r7QyM62…>> _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1dS-NlFBksiulwBVJ54OgNH06JWJ8AG7AYE-cayHfJPVbT… <https://secure-web.cisco.com/12RCdM4nvnTq08RfLMdhWLNUwwCLn6K8WftCJlAbuQ-Iak…> -------------- next part -------------- An HTML attachment was scrubbed... URL: *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* http://secure-web.cisco.com/1hIgnRBX_cCUDKR7QqaLiJ_PdchI690J0vHLQTbYqRvEno2… <http://secure-web.cisco.com/1-ElI_7sKqW6lxkAwWOez-HtzoPs3XaGEhhUrCO29Bdd5NW…> ------------------------------ Message: 18 Date: Tue, 6 Apr 2021 13:38:37 +0000 From: Daniel Gutstein <daniel.gutstein(a)northwestern.edu> Subject: [Freesurfer] Freesurfer Versions - Zeros in the Cortex To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <2F5F4F23-A758-4F12-B303-EBD66FEF346F(a)northwestern.edu> Content-Type: text/plain; charset="utf-8" ??????? External Email - Use Caution Hello, We are looking at the vertex-wise thickness measures for participants within the fsaverage space. There are a number of indices within the cortex that have thickness values of 0 in the thickness.fsaverage.mgh surface files. In FreeSurfer version 5.1, those same indices no longer have thickness 0 in the corresponding rh and lh fwhm smoothed thickness surface files due to the smoothing effect. However, in versions 6 and 7.1.1, the indices with 0 values remain 0 even in the fwhm smoothed files. Do you know why it was chosen that smoothing should have no impact on zeros in the later versions of FreeSurfer? Also, if we are interested in impacting the zeros from the later versions, is there a methodology which you would recommend? Thanks, Daniel -------------- next part -------------- An HTML attachment was scrubbed... URL: *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* http://secure-web.cisco.com/1eH10j7MaLjBuzRMQDr8HDVm_84aJo_QppGXt6lWy-K8eVw… <http://secure-web.cisco.com/1qJ7J-gsyCyG4W7J2Uy0j8sJ6RnzfO2PQyYExeP1IkO8Q1g…> ------------------------------ Message: 19 Date: Tue, 6 Apr 2021 15:41:36 +0200 From: Bahar Hazal Yal??nkaya <baharhazalyalcinkaya(a)gmail.com> Subject: Re: [Freesurfer] mri_gtmpvc error Checking tissue type ERROR: ??????? CheckSegTissueType() tissue type for seg To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <CAGZFL9eVvG1+FhoUqK24DG=ahiMfYhQ2AGA5UbzfXDHZKA056g(a)mail.gmail.com> Content-Type: text/plain; charset="utf-8" ??????? External Email - Use Caution Thanks for response, color table and annotations are there "--ctx-annot Schaefer2018_400Parcels_7Networks_order.annot 1000 2000 --ctab Schaefer2018_400Parcels_7Networks_order_LUT.txt", gtmseg did not gave an error, you can see at attachments. (Also I can see 258 Head segmentation in *gtmseg.ctab *file) also mri_coreg is working well (see also attachments). The problem is the "*mri_gtmpvc*" command where it fails while checking tissue types more precisely it complains about Head segmentation. I run with standard options. I checked everything I can think of, each file and image seems to be similar but still could not find a proper solution. Is there anything specific I need to check? Thanks in advance, Kind regards On Tue, Apr 6, 2021 at 3:26 PM Douglas N. Greve <dgreve(a)mgh.harvard.edu> wrote: You will need to create a new color table. This is not hard, but not easy either. First, there should be a color table already there. I'm not sure what that will be like; it might have your segments in it, it might not. It might be easier to run gtmseg with the standard options and look at the color table, then try to replicate it with your segmentation On 4/5/2021 6:43 AM, Bahar Hazal Yal??nkaya wrote: ???????? External Email - Use Caution Hello Freesurfer"s Developers, I am trying to follow *PetSurfer* (*MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1MVnuTs8K837n1EabeVA8Fk2FSlKYqIyoMOZLNUEUFjVIs… <https://secure-web.cisco.com/1MVnuTs8K837n1EabeVA8Fk2FSlKYqIyoMOZLNUEUFjVIs…> <https://secure-web.cisco.com/1oGyZvXtztP0MX30hKqio2fJStw1wQuIW11p5b1b0CkNwS… <https://secure-web.cisco.com/1oGyZvXtztP0MX30hKqio2fJStw1wQuIW11p5b1b0CkNwS…>>) to apply PVC to Pet images. Default pipeline is working however, whenever i try to use another atlas, Schaefer parcellation, mri_gtmpvc command I get following error: WARNING: LTAconcat(): inverting LTA 1 to match geometry Replacing 18 Pruning ctab tissue type schema Checking tissue type ERROR: CheckSegTissueType() tissue type for seg 258 Head-ExtraCerebral not set Failed tissue type check I have searched to list several people who have issued similar errors but unfortunately i could not find any solution that works for me. Below you can find commands I used: $ gtmseg --s subject --o gtmseg.mgz --ctx-annot Schaefer2018_400Parcels_7Networks_order.annot 1000 2000 --ctab Schaefer2018_400Parcels_7Networks_order_LUT.txt $ mri_coreg --s subject --mov AbetaPre.nii.gz --reg AbetaPre.reg.lta $ mri_gtmpvc --i AbetaPre.nii.gz --psf 8 --reg AbetaPre.reg.lta --regheader --seg gtmseg.mgz --default-seg-merge --auto-mask PSF .01 --mgx .01 --km-ref 8 47 --o gtmpvc.output Also I checked the run of gtmseg via "*tkmeditfv*" where i can visualise 258 Head-ExtraCerebral, and additionally I checked *gtmseg.ctab *file also 258 Head-ExtraCerebral in the list. I will be happy to hear from you. Kind regards. -- Ph.D. Bahar Hazal Yal??nkaya _______________________________________________ Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://secure-web.cisco.com/14cq6eGfvOcpfd9Y3vfBGA7p9Xc5PZeusO6xBxdl8k8go_… <https://secure-web.cisco.com/14cq6eGfvOcpfd9Y3vfBGA7p9Xc5PZeusO6xBxdl8k8go_…> -- Ph.D. Bahar Hazal Yal??nkaya -------------- next part -------------- An HTML attachment was scrubbed... URL: *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* http://secure-web.cisco.com/1S2lCNb1gnc5pjrdGt-w4c8k9xnz2e21mxk33QLcXZJytlK… <http://secure-web.cisco.com/1WIhGAvTXV9Ra_j9997UQvU-t9D5OdG2kP8Cwneiyynbya0…> -------------- next part -------------- A non-text attachment was scrubbed... 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URL: http://secure-web.cisco.com/12vEUaoJc5rBuZIL2Phmoh-cd7WLFexhuj0xkZjbkvwn_Sy… ------------------------------ Message: 5 Date: Thu, 15 Apr 2021 10:01:38 -0400 From: "Douglas N. Greve" <dgreve(a)mgh.harvard.edu> Subject: Re: [Freesurfer] Surface registration problem To: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <87b2dec1-21cb-c4f0-4ff5-e1d6d49284c9(a)mgh.harvard.edu> Content-Type: text/plain; charset=utf-8; format=flowed This means that the source or target of the registration is not the same as what is in the registration file. Did the subject folder change? You can always delete the registration and rerun, and it will register to the new target On 4/9/2021 10:58 AM, Manenti, Giorgio wrote: External Email - Use Caution Dear Experts, I?m encountering a problem when running the preproc-sess on my functional data. When using the flag -surface subject hemi i am getting ":ERROR: source volume is neither source nor target of the registration?. The source is a template.nii file present in the bold folders, while the destination file is the mri/orig.mgz from the ?subject? folder (after Longitudinal recon-all). I am not sure if the problem could be connected with the mc-sess,stc-sess or topup (where i need to crop out 1 slice to get an even volume) steps, that i?m running before preproc-sess, or if i?m missing an extra flag. Here the command i?m running: preproc-sess -s f10_sess01new -fsd bold -i my_hifi_images -nostc -nomc -surface hum_15721.long.long010 lhrh -mni305 -fwhm 4 -per-run Many thanks for your time and support, Best Regards Giorgio _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://secure-web.cisco.com/1dS-NlFBksiulwBVJ54OgNH06JWJ8AG7AYE-cayHfJPVbT… ------------------------------ Message: 6 Date: Thu, 15 Apr 2021 10:04:21 -0400 From: "Douglas N. Greve" <dgreve(a)mgh.harvard.edu> Subject: Re: [Freesurfer] aparc+aseg to native space issue To: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <90cf6e25-0f0a-3354-622a-bf6c326cabb3(a)mgh.harvard.edu> Content-Type: text/plain; charset="windows-1252" What are the voxel sizes in the native space? It may be that if it were shifted one voxel over, it would be shifted too far in the other direction. On 4/12/2021 10:42 AM, Larson, Kathleen E wrote: ????????External Email - Use Caution ????????External Email - Use Caution Hi again, I realized that it may be helpful if I include some images to show what I mean when I say ?slightly offset?. In the image attached are 2 T1w images overlayed with the right WM thresholded from the aparc+aseg image. On the left is the native space, and the right is in FS space. You can see a slight shift in the segmentation on the left compared to the native space on the right. (I?m using the thresholded WM from the aparc+aseg because it?s easier to see the offset than with the entire segmentation). Please let me know if you have any suggestions for how to correct this! Katie Larson *From:* freesurfer-bounces(a)nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> *On Behalf Of *Larson, Kathleen E *Sent:* Wednesday, April 7, 2021 4:24 PM *To:* freesurfer(a)nmr.mgh.harvard.edu *Subject:* [Freesurfer] aparc+aseg to native space issue Hi, I am having an issue converting the aparc+aseg segmentation into the native space. I have tried using both of the following commands: mri_label2vol --seg aparc+aseg.mgz --temp rawavg.mgz --o aparc+aseg_native.mgz --regheader mri_vol2vol --mov aparc+aseg.mgz --targ rawavg.mgz --regheader --nearest --o aparc+aseg_native.mgz In both cases, the output segmentation in native space is slightly offset along the x axis (given x,y,z coordinates). In fact, mri_label2vol is offset in the opposite direction as mri_vol2vol. All outputs have the same origin as the original native space, so I am wondering if it?s a problem with the interpolation. Do you have any advice for how to fix this issue? Thank you! Kathleen Larson (she/her) Medical Image Computing Lab (MedICL) Biomedical Engineering | Ph.D. Candidate Vanderbilt University _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://secure-web.cisco.com/1AYz_sY6PNdA4zpLiadZj9Jo25NItNLJYarDRNK_o7RxTV… -------------- next part -------------- An HTML attachment was scrubbed... URL: http://secure-web.cisco.com/1bTG-LMLs5M_cc1_mtnEvSjuXMnNWr2gmUtyTdJwGPNOels… ------------------------------ Message: 7 Date: Thu, 15 Apr 2021 10:06:50 -0400 From: "Douglas N. Greve" <dgreve(a)mgh.harvard.edu> Subject: Re: [Freesurfer] mkcontrast2 typo in 7.1.1 To: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <a500afd4-5383-a3f2-e1f2-c99b147fdedd(a)mgh.harvard.edu> Content-Type: text/plain; charset=utf-8; format=flowed Thanks, I just fixed it and pushed the change. Should be in the next version. On 4/12/2021 3:05 PM, Ben Singer wrote: External Email - Use Caution On line 106: if($FS_MKCON_USE_BIN == 0 && UseOctave == 0) then there should be a "$" before the "UseOctave" to make the line read: if($FS_MKCON_USE_BIN == 0 && $UseOctave == 0) then Apologies if this has been already corrected, I didn't come across this in an archive search. It looks like this bug originated in July 2018, and is the reason for a few 2019 and one or two 2020 posts complaining of "MATLAB: variable undefined" errors. Below here is just some more background info about what sort of errors might result, and why setting the MATLAB variable to the matlab executable works around the problem, but causes a new problem with the mex command. The conditional is always false before the fix-- so the MATLAB variable is never set to whatever fsfast's "getmatlab" function assigns to it, in the body of the conditional. So this could be the source of several "MATLAB: Undefined variable" errors reported on this list. If one sets the MATLAB environment variable to the "R20xx/bin/matlab" executable , one can work around this problem. But-- the Matlab "mex" command uses the MATLAB variable, and expects it to be set to the Matlab root directory in order to determine the machine architecture for your host (type "mex" at the shell prompt when MATLAB is set to the matlab executable, to see the error message.) Setting the MATLAB variable the way the "mex" command expects would then result in "/path/to/R20xx: permission denied" errors when running mkcontrast-related scripts. Sorry for the wordiness. Bottom line is dollar sign. _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://secure-web.cisco.com/1dS-NlFBksiulwBVJ54OgNH06JWJ8AG7AYE-cayHfJPVbT… ------------------------------ Message: 8 Date: Thu, 15 Apr 2021 10:09:23 -0400 From: "Douglas N. Greve" <dgreve(a)mgh.harvard.edu> Subject: Re: [Freesurfer] mri_segstats to report empty and non-empty segmentation To: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <2110d774-d5c7-de45-5803-6769f09ef7f9(a)mgh.harvard.edu> Content-Type: text/plain; charset="utf-8" Try adding --empty On 4/12/2021 4:58 PM, miracle ozzoude wrote: ????????External Email - Use Caution Hello Experts, I am using mri_segstats with the --ctab flag to extract dti and suvr values from a white matter hyperintensities parcellation. Running mri_segstats on the image and parcellation with --ctab only reports on non-empty segmentations. I want it to also report on the empty segmentations. Is there a flag or any other freesurfer commands that i can use? Summary: I want mri_segstats to report on non-empty and empty segmentations, not just the former. Cheers. || |cmdline mri_segstats --seg wmh_lobar.nii.gz --i subj_rescaled_wholecere_PET2T1_smooth.nii.gz --sum SUVR_WMH_lobar.stats --ctab WMColorLUT.ctab --pv norm.mgz| |Loading wmh_lobar.nii.gz| |INFO: using NIfTI-1 qform| |Loading subj_rescaled_wholecere_PET2T1_smooth.nii.gz| |Loading norm.mgz| |Voxel Volume is 1 mm^3| |Generating list of segmentation ids| |Found 13 segmentations| |Computing statistics for each segmentation||Reporting on 11 segmentations| |Using PrintSegStat| |mri_segstats done| _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://secure-web.cisco.com/1dS-NlFBksiulwBVJ54OgNH06JWJ8AG7AYE-cayHfJPVbT… -------------- next part -------------- An HTML attachment was scrubbed... URL: http://secure-web.cisco.com/1frwpFS2RG_gT3UY0UCkk3IBi2H-mMV6J-R9gxET9fjL1di… ------------------------------ Message: 9 Date: Thu, 15 Apr 2021 10:10:26 -0400 From: "Douglas N. Greve" <dgreve(a)mgh.harvard.edu> Subject: Re: [Freesurfer] Subthalamic nucleus volume (Douglas N. Greve) To: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <372a67f2-828f-f654-12f1-0cb0cef42f62(a)mgh.harvard.edu> Content-Type: text/plain; charset="windows-1252" Sorry, which email is this referring to? On 4/12/2021 5:58 PM, T. Pansuwan wrote: ????????External Email - Use Caution ????????External Email - Use Caution Dear Douglas, Thank you for your reply. Could you possibly elaborate more on how this method will only reflect the registration in that area instead of volume? I got this method from freesurfer tutorial on obtaining custom anatomical ROI analysis. And do you have any suggestion on an alternative method to accurately obtain sub thalamic nucleus volume? Best wishes, Tanrada On 5 Apr 2021, at 17:00, freesurfer-request(a)nmr.mgh.harvard.edu <mailto:freesurfer-request@nmr.mgh.harvard.edu> wrote: Send Freesurfer mailing list submissions to freesurfer(a)nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> To subscribe or unsubscribe via the World Wide Web, visit https://secure-web.cisco.com/1dS-NlFBksiulwBVJ54OgNH06JWJ8AG7AYE-cayHfJPVbT… or, via email, send a message with subject or body 'help' to freesurfer-request(a)nmr.mgh.harvard.edu You can reach the person managing the list at freesurfer-owner(a)nmr.mgh.harvard.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of Freesurfer digest..." Today's Topics: ??1. Dicom Tag Problem Reconall (Banu Femir) ??2. mri_vol2surf empty output (Karan Desai) ??3. mri_gtmpvc error Checking tissue type ERROR: ?????CheckSegTissueType() tissue type for seg (Bahar Hazal Yal??nkaya) ??4. Re: make_average_subject error (Douglas N. Greve) ??5. Re: Running recon-all with FLAIR (Douglas N. Greve) ??6. Re: functional to anatomical registration question ?????(Douglas N. Greve) ??7. Re: Problem with freesurfer measures (Douglas N. Greve) ??8. Re: ERROR: Cannot find stats file (Douglas N. Greve) ??9. Re: Subthalamic nucleus volume (Douglas N. Greve) ?10. Re: Talairach Failed: Distorted T1 (Douglas N. Greve) ?11. Re: quantification of volume of perivascular spaces ?????(Douglas N. Greve) ?12. "ERROR: crypt() returned null with 4-line file" (Cook, Philip) ?13. Re: Problem with freesurfer measures (Alberto Del Cerro Leon) ---------------------------------------------------------------------- Message: 1 Date: Sun, 4 Apr 2021 22:57:57 +0300 From: Banu Femir <banu.femir(a)gmail.com> Subject: [Freesurfer] Dicom Tag Problem Reconall To: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <CANuRgTpGaqjYJVd9V+n3-82ASsx0uP=S=3dH5ksxoxda34S3gA(a)mail.gmail.com> Content-Type: text/plain; charset="utf-8" ???????External Email - Use Caution Dear Freesurfer Developers, I'm trying to analyze a set of MRI data that I got via CD. Dicom files did not have .dcm extension, so I used a program and they turned into a .dcm image. My reconall run for around 2 hours, after I got an error: Counting frames nframes = 481 nslices = 1 ndcmfiles = 481 PE Dir = UNKNOWN (dicom read) Loading pixel data JPEG compressed, decompressing cd /home/banu/usr/local/freesurfer/subjects/sepsis1dicomwritebelow fsdcmdecompress --i /home/banu/Documents/Sepsis/yeni_dicom_write_below/F_000001.dcm --o /tmp/banu.tmp.decompressed.dcm.1TXZUy --jpeg >& /tmp/banu.tmp.decompressed.dcm.1TXZUy.dcmdjpeg.out ERROR: 512, see /tmp/banu.tmp.decompressed.dcm.1TXZUy.dcmdjpeg.out for more details Linux banuf 4.15.0-51-generic #55-Ubuntu SMP Wed May 15 14:27:21 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux Before that, I got many Warnings about imagenumber, tag serial number, seriesnumber, tag, ect. In case you want I can share the whole log file. I am wondering if there was sth wrong with my .dcm format. If yes, how I can solve this problem? It seems like there was sth wrong with tags, but I really cannot solve the problem. Many thanks! Have a nice and healthy week! Banu -------------- next part -------------- An HTML attachment was scrubbed... URL: http://secure-web.cisco.com/15vtLxaXUmJCCnTlFjiq9NOy4ZPi19OKJMVBFuZNS-qz6U5… ------------------------------ Message: 2 Date: Mon, 5 Apr 2021 04:09:07 +0000 From: Karan Desai <karan.desai(a)duke.edu> Subject: [Freesurfer] mri_vol2surf empty output To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <DM6PR05MB40096B471BBB697482E1939E9C779(a)DM6PR05MB4009.namprd05.prod.outlook.com> Content-Type: text/plain; charset="iso-8859-1" ???????External Email - Use Caution Hi FS Forum, I am posting because after using the command mri_vol2surf to downsample my scans to fsaverage4, I ended up with empty files when viewed in Freeview. This is the command that I ran generally: mri_vol2surf --src bold_preproc.nii.gz --out lh.imagename.nii.gz --regheader sub-01 --trgsubject fsaverage4 -hemi lh I am assuming there are some tags that I may be missing which are leading me to output with empty nii.gz files. The input bold preprocessed files are viewed normally in Freeview, but the output is empty. Thank you in advance. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://secure-web.cisco.com/1kkITcg9V3aoaMTZdLkQAOvSvP1dy3BzVYL9bPzOwZuBRPA… ------------------------------ Message: 3 Date: Mon, 5 Apr 2021 12:43:18 +0200 From: Bahar Hazal Yal??nkaya <baharhazalyalcinkaya(a)gmail.com> Subject: [Freesurfer] mri_gtmpvc error Checking tissue type ERROR: CheckSegTissueType() tissue type for seg To: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <CAGZFL9cpgOZFDSYndyJg0T4=dbd8Fvk5TwHUJGLYUQg+363SCw(a)mail.gmail.com> Content-Type: text/plain; charset="utf-8" ???????External Email - Use Caution Hello Freesurfer"s Developers, I am trying to follow *PetSurfer* ( https://secure-web.cisco.com/1oGyZvXtztP0MX30hKqio2fJStw1wQuIW11p5b1b0CkNwS…) to apply PVC to Pet images. Default pipeline is working however, whenever i try to use another atlas, Schaefer parcellation, mri_gtmpvc command I get following error: WARNING: LTAconcat(): inverting LTA 1 to match geometry Replacing 18 Pruning ctab tissue type schema Checking tissue type ERROR: CheckSegTissueType() tissue type for seg 258 Head-ExtraCerebral not set Failed tissue type check I have searched to list several people who have issued similar errors but unfortunately i could not find any solution that works for me. Below you can find commands I used: $ gtmseg --s subject --o gtmseg.mgz --ctx-annot Schaefer2018_400Parcels_7Networks_order.annot 1000 2000 --ctab Schaefer2018_400Parcels_7Networks_order_LUT.txt $ mri_coreg --s subject --mov AbetaPre.nii.gz --reg AbetaPre.reg.lta $ mri_gtmpvc --i AbetaPre.nii.gz --psf 8 --reg AbetaPre.reg.lta --regheader --seg gtmseg.mgz --default-seg-merge --auto-mask PSF .01 --mgx .01 --km-ref 8 47 --o gtmpvc.output Also I checked the run of gtmseg via "*tkmeditfv*" where i can visualise 258 Head-ExtraCerebral, and additionally I checked *gtmseg.ctab *file also 258 Head-ExtraCerebral in the list. I will be happy to hear from you. Kind regards. -- Ph.D. Bahar Hazal Yal??nkaya -------------- next part -------------- An HTML attachment was scrubbed... URL: http://secure-web.cisco.com/1igHEuXb57vbO5luReQnJUZlS8N4UiSy6PzXb6ZxaMvM-G_… ------------------------------ Message: 4 Date: Mon, 5 Apr 2021 09:43:06 -0400 From: "Douglas N. Greve" <dgreve(a)mgh.harvard.edu> Subject: Re: [Freesurfer] make_average_subject error To: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <957177a6-1c79-0149-4cbd-1a16122cd203(a)mgh.harvard.edu> Content-Type: text/plain; charset="utf-8" It looks like you are still using the old make_average_subject as the time stamp is from Jan 19, 2017 (same for mri_aparc2aseg). Can you confirm that those are really the patches? On 3/29/2021 12:52 PM, Jordan Mullins wrote: ????????External Email - Use Caution Hi Douglas, Just following up on this. Thanks! On Wed, Mar 17, 2021 at 6:12 PM Jordan Mullins <jordan.mullins(a)email.ucr.edu <mailto:jordan.mullins@email.ucr.edu>> wrote: ???Yes! Results attached. ???On Wed, Mar 17, 2021 at 5:54 PM Douglas N. Greve ???<dgreve(a)mgh.harvard.edu <mailto:dgreve@mgh.harvard.edu>> wrote: ???????Can you run ???????ls -l $FREESURFER_HOME/bin/mri_aparc2aseg ???????$FREESURFER_HOME/bin/make_average_subject ???????and send the result? ???????Also, the result of ???????which mri_aparc2aseg ???????which make_average_subject ???????On 3/17/2021 8:36 PM, Jordan Mullins wrote: ???????????????External Email - Use Caution ???????Yes, I had seen that report and had downloaded the patch, but ???????still got the same error. Are there any other steps I can take? ???????On Wed, Mar 17, 2021 at 2:59 PM Douglas N. Greve ???????<dgreve(a)mgh.harvard.edu <mailto:dgreve@mgh.harvard.edu>> wrote: ???????????This problem is documented (along with a fix) on our ???????????release notes ???????????*MailScanner has detected a possible fraud attempt from ???????????"secure-web.cisco.com" claiming to be* ???????????https://secure-web.cisco.com/1FxB5IO1KfdsWRKWGZCaZ1DejNOIQVqTCyvipHybDiqadllTrFr5h04djSAlRl993WytrR919HibdPhKwsTuw32Hp9Es3KEhTSk0b5y7aF-UNCcjyBPNzOhD-11jGBfHLKyHOourvwZQdylxu-HLIqIniYy7cLMZjYQcOtqOkQ_EGUlxpxpapULJGUd6fyfxtzky_gyeGmxuyO6q8XMMr0MlmFk578-5tZKTPA43VX1r7v0_RXGIGT9kW7Kw2Gvrv1e1W3KTIIY46ZozWFLqhWA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FReleaseNotes ???????????<https://secure-web.cisco.com/1-guBCff1jWC1GKEt4a1kTf7-FWdC1pS-TRdvmtUoD4S5H…> ???????????On 3/16/2021 3:39 PM, Jordan Mullins wrote: ???????????????????External Email - Use Caution ???????????Yes, I used the make_average_subject command. I've ???????????attached a text file below of the command line and ???????????terminal output from my attempt to average two subjects. ???????????I get the same error when I try this with the full sample. ???????????On Tue, Mar 16, 2021 at 9:12 AM Douglas N. Greve ???????????<dgreve(a)mgh.harvard.edu <mailto:dgreve@mgh.harvard.edu>> ???????????wrote: ???????????????What command are you using? make_average_subject? ???????????????Send the command line and terminal output ???????????????On 3/10/2021 3:53 PM, Jordan Mullins wrote: ???????????????????????External Email - Use Caution ???????????????Hello, ???????????????I am trying to create an average subject from a set ???????????????of subjects, but keep getting an error that says ???????????????"mghRead(mri/norm.mgz, -1): could not open file". ???????????????I've read that several others have solved this ???????????????issue by installing the patch available at ???????????????*MailScanner has detected a possible fraud attempt ???????????????from "secure-web.cisco.com" claiming to be* ???????????????http://secure-web.cisco.com/1neOj3ezV1FYP4da5emtXutE0czMFgBMgwiC2rSEOqXvhKtBY9wqXzbbxTppcarixu07YDjIN441Dr-36aYpuEwUYt0ewSizoYBAF0BNTmUOTBAwD3O54TDqbyqsXUsBb8KS8cdEEe4R0x0aOwlz2JNu0Z7RyQ8JqoxbDeqi43szAJt2W2ifGhsbj3JT-33Gs8t9n6FP3Vp8hWhVRtAzXaLWSo2DVDrBJ9EycOZOcJRd6IZzPJa-TF9EdlA_k_YHimtX0LwZt6LB8xLk2pU1gaQ/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2F6.0.0-patch%2F ???????????????<http://secure-web.cisco.com/1holHARxUGo27ZLvlj5vX0sbezsRgmRaNdE1T-Z728EASqG…>. ???????????????I did this, but continue to get the same error. I'm ???????????????working with Freesurver Version 6.0.0 and MacOS Big ???????????????Sur Version 11.2.3. I've attached the recon-all.log ???????????????below, but please let me know if you need ???????????????additional information. ???????????????Any insight on this would be appreciated! Thank you! ???????????????Jordan ???????????????-- ???????????????*Jordan L. Mullins, B.A.* ???????????????Doctoral Student, Department of Psychology ???????????????University of California, Riverside ???????????????*MailScanner has detected a possible fraud attempt ???????????????from "secure-web.cisco.com" claiming to be* ???????????????http://secure-web.cisco.com/1e0sWiIUaoVgvvDE3QqhHprkkvMCKHgk4v4Y5oITYWtFEUrXnBjbnllWzRQfL7ukIhir08wLXQ_8ZtoCz596ui-2wPYWC6mfH5PC7GBvNqH_iREmvK4Eyn3lRFh1WWyLs7okWZuIFAQ5gSEqJNCX8zacPDJnGs8aPmEKMuKRRn9UOege1rUQ0IyMWPM6FZLP_olADZ7arMqOXQwRHNfsBrD6rUxIUrfW7vyt8Galf3qlqosYl9fzT8KQ4GGiwQcnsgAsObCWyeUTvKn2T1Sxu7w/http%3A%2F%2Fucrkindlab.com ???????????????<http://secure-web.cisco.com/1mshZJHsrG2WjtWWNRNV7vunyA6LicMMo4DqXl-CgSaJWwH…> ???????????????_______________________________________________ ???????????????Freesurfer mailing list ???????????????Freesurfer(a)nmr.mgh.harvard.edu ?<mailto:Freesurfer@nmr.mgh.harvard.edu> ???????????????*MailScanner has detected a possible fraud attempt ???????????????from "secure-web.cisco.com" claiming to be* ???????????????https://secure-web.cisco.com/1dS-NlFBksiulwBVJ54OgNH06JWJ8AG7AYE-cayHfJPVbTKex0CQR6WnJqjC8JoIzm7_eMdZsL6Y54UFodC6LZcy4JWJg5_k7FoHtCpK14QFsSMWuVml81c-ZC6szy6iUl8iYVNKOahK3dZIeSvKyXtN9O0bUmOror7aJKZGwA75UZPrkLIbJDp0-twu0MLfoiBoBPN4BcSKoeS8xmCAzARi21Cp7P_Z1EOAQOd01fJm_cNqXdC3vohizq8JwmgScCHN3G2rnnVhQ_zkLnFRdlA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer ?<https://secure-web.cisco.com/10GU0iklq7S5a2rmbF5WWPuOiSuT2PW57w03wJKzHnXHAa…> ???????????????_______________________________________________ ???????????????Freesurfer mailing list ???????????????Freesurfer(a)nmr.mgh.harvard.edu ???????????????<mailto:Freesurfer@nmr.mgh.harvard.edu> ???????????????*MailScanner has detected a possible fraud attempt ???????????????from "secure-web.cisco.com" claiming to be* ???????????????https://secure-web.cisco.com/1dS-NlFBksiulwBVJ54OgNH06JWJ8AG7AYE-cayHfJPVbTKex0CQR6WnJqjC8JoIzm7_eMdZsL6Y54UFodC6LZcy4JWJg5_k7FoHtCpK14QFsSMWuVml81c-ZC6szy6iUl8iYVNKOahK3dZIeSvKyXtN9O0bUmOror7aJKZGwA75UZPrkLIbJDp0-twu0MLfoiBoBPN4BcSKoeS8xmCAzARi21Cp7P_Z1EOAQOd01fJm_cNqXdC3vohizq8JwmgScCHN3G2rnnVhQ_zkLnFRdlA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer ???????????????<https://secure-web.cisco.com/10GU0iklq7S5a2rmbF5WWPuOiSuT2PW57w03wJKzHnXHAa…> ???????????-- ???????????*Jordan L. Mullins, B.A.* ???????????Doctoral Student, Department of Psychology ???????????University of California, Riverside ???????????*MailScanner has detected a possible fraud attempt from ???????????"secure-web.cisco.com" claiming to be* ???????????http://secure-web.cisco.com/1e0sWiIUaoVgvvDE3QqhHprkkvMCKHgk4v4Y5oITYWtFEUrXnBjbnllWzRQfL7ukIhir08wLXQ_8ZtoCz596ui-2wPYWC6mfH5PC7GBvNqH_iREmvK4Eyn3lRFh1WWyLs7okWZuIFAQ5gSEqJNCX8zacPDJnGs8aPmEKMuKRRn9UOege1rUQ0IyMWPM6FZLP_olADZ7arMqOXQwRHNfsBrD6rUxIUrfW7vyt8Galf3qlqosYl9fzT8KQ4GGiwQcnsgAsObCWyeUTvKn2T1Sxu7w/http%3A%2F%2Fucrkindlab.com ???????????<http://secure-web.cisco.com/1isz3Mv28M3mhtt4WMtIi4EdyCh_c32He7_-DHAGSjuicnh…> ???????????_______________________________________________ ???????????Freesurfer mailing list ???????????Freesurfer(a)nmr.mgh.harvard.edu ?<mailto:Freesurfer@nmr.mgh.harvard.edu> ???????????*MailScanner has detected a possible fraud attempt from ???????????"secure-web.cisco.com" claiming to be* ???????????https://secure-web.cisco.com/1dS-NlFBksiulwBVJ54OgNH06JWJ8AG7AYE-cayHfJPVbTKex0CQR6WnJqjC8JoIzm7_eMdZsL6Y54UFodC6LZcy4JWJg5_k7FoHtCpK14QFsSMWuVml81c-ZC6szy6iUl8iYVNKOahK3dZIeSvKyXtN9O0bUmOror7aJKZGwA75UZPrkLIbJDp0-twu0MLfoiBoBPN4BcSKoeS8xmCAzARi21Cp7P_Z1EOAQOd01fJm_cNqXdC3vohizq8JwmgScCHN3G2rnnVhQ_zkLnFRdlA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer ?<https://secure-web.cisco.com/18ekJrFGSKJvrjW_N8XnUIHQ7WEdFV8flsrhGU5xVLbtdo…> ???????????_______________________________________________ ???????????Freesurfer mailing list ???????????Freesurfer(a)nmr.mgh.harvard.edu ???????????<mailto:Freesurfer@nmr.mgh.harvard.edu> ???????????*MailScanner has detected a possible fraud attempt from ???????????"secure-web.cisco.com" claiming to be* ???????????https://secure-web.cisco.com/1dS-NlFBksiulwBVJ54OgNH06JWJ8AG7AYE-cayHfJPVbTKex0CQR6WnJqjC8JoIzm7_eMdZsL6Y54UFodC6LZcy4JWJg5_k7FoHtCpK14QFsSMWuVml81c-ZC6szy6iUl8iYVNKOahK3dZIeSvKyXtN9O0bUmOror7aJKZGwA75UZPrkLIbJDp0-twu0MLfoiBoBPN4BcSKoeS8xmCAzARi21Cp7P_Z1EOAQOd01fJm_cNqXdC3vohizq8JwmgScCHN3G2rnnVhQ_zkLnFRdlA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer ???????????<https://secure-web.cisco.com/18ekJrFGSKJvrjW_N8XnUIHQ7WEdFV8flsrhGU5xVLbtdo…> ???????-- ???????*Jordan L. Mullins, B.A.* ???????Doctoral Student, Department of Psychology ???????University of California, Riverside ???????*MailScanner has detected a possible fraud attempt from ???????"secure-web.cisco.com" claiming to be* http://secure-web.cisco.com/1e0sWiIUaoVgvvDE3QqhHprkkvMCKHgk4v4Y5oITYWtFEUr… ???????<http://secure-web.cisco.com/1Hb5eBrObpHBXZQD2S7ILWEKBRwR7OK46HlRQPn5nJhb1RK…> ???????_______________________________________________ ???????Freesurfer mailing list ???????Freesurfer(a)nmr.mgh.harvard.edu ?<mailto:Freesurfer@nmr.mgh.harvard.edu> ???????*MailScanner has detected a possible fraud attempt from ???????"secure-web.cisco.com" claiming to be* ???????https://secure-web.cisco.com/1dS-NlFBksiulwBVJ54OgNH06JWJ8AG7AYE-cayHfJPVbTKex0CQR6WnJqjC8JoIzm7_eMdZsL6Y54UFodC6LZcy4JWJg5_k7FoHtCpK14QFsSMWuVml81c-ZC6szy6iUl8iYVNKOahK3dZIeSvKyXtN9O0bUmOror7aJKZGwA75UZPrkLIbJDp0-twu0MLfoiBoBPN4BcSKoeS8xmCAzARi21Cp7P_Z1EOAQOd01fJm_cNqXdC3vohizq8JwmgScCHN3G2rnnVhQ_zkLnFRdlA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer ?<https://secure-web.cisco.com/19urZV244XBN3c3mH4I2cxDmyxpusIxBLp95shYeNJALWi…> ???????_______________________________________________ ???????Freesurfer mailing list ???????Freesurfer(a)nmr.mgh.harvard.edu ???????<mailto:Freesurfer@nmr.mgh.harvard.edu> ???????*MailScanner has detected a possible fraud attempt from ???????"secure-web.cisco.com" claiming to be* ???????https://secure-web.cisco.com/1dS-NlFBksiulwBVJ54OgNH06JWJ8AG7AYE-cayHfJPVbTKex0CQR6WnJqjC8JoIzm7_eMdZsL6Y54UFodC6LZcy4JWJg5_k7FoHtCpK14QFsSMWuVml81c-ZC6szy6iUl8iYVNKOahK3dZIeSvKyXtN9O0bUmOror7aJKZGwA75UZPrkLIbJDp0-twu0MLfoiBoBPN4BcSKoeS8xmCAzARi21Cp7P_Z1EOAQOd01fJm_cNqXdC3vohizq8JwmgScCHN3G2rnnVhQ_zkLnFRdlA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer ???????<https://secure-web.cisco.com/19urZV244XBN3c3mH4I2cxDmyxpusIxBLp95shYeNJALWi…> ???-- ???*Jordan L. Mullins, B.A.* ???Doctoral Student, Department of Psychology ???University of California, Riverside ???*MailScanner has detected a possible fraud attempt from ???"secure-web.cisco.com" claiming to be* http://secure-web.cisco.com/1e0sWiIUaoVgvvDE3QqhHprkkvMCKHgk4v4Y5oITYWtFEUr… ???<http://secure-web.cisco.com/1fpwAcAdfpPcgXwG26yDXqSP95kASeRHLMrJFeIUyDibUdq…> -- *Jordan L. Mullins, B.A.* Doctoral Student, Department of Psychology University of California, Riverside *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* http://secure-web.cisco.com/1e0sWiIUaoVgvvDE3QqhHprkkvMCKHgk4v4Y5oITYWtFEUr… <http://secure-web.cisco.com/1fpwAcAdfpPcgXwG26yDXqSP95kASeRHLMrJFeIUyDibUdq…> _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://secure-web.cisco.com/1dS-NlFBksiulwBVJ54OgNH06JWJ8AG7AYE-cayHfJPVbT… -------------- next part -------------- An HTML attachment was scrubbed... URL: http://secure-web.cisco.com/1m766OV31S4YEy1xGWnbfNAAYOLYpUbh-B0OqLiXOaGIKvV… ------------------------------ Message: 5 Date: Mon, 5 Apr 2021 09:45:47 -0400 From: "Douglas N. Greve" <dgreve(a)mgh.harvard.edu> Subject: Re: [Freesurfer] Running recon-all with FLAIR To: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <26935515-0e6a-2960-9fe4-e7fb16ebf265(a)mgh.harvard.edu> Content-Type: text/plain; charset="utf-8" Try this cd subject/mri mri_coreg --i orig/T2raw.mgz --targ orig.mgz --reg transforms/T2raw.lta You can run with multiple threads by adding --threads N where N is the number of threads On 3/29/2021 5:18 PM, Edina Szab? wrote: ????????External Email - Use Caution Dear All, We are running recon-all on the latest version of FreeSurfer (v7.1.1). We are using both T1 and FLAIR images to better define the pial surfaces, but when we run the recommended command line (recon-all -subject subjectname -i /path/to/input_volume -FLAIR /path/to/FLAIR_volume -FLAIRpial -all) the pial surface is very underestimated (?.pial.FLAIR ? and the aseg volume is based on these surfaces), and we get better results without the FLAIR. It seems that FreeSurfer mis-registers the FLAIR to the T1 during the process. Is there a separate step we should do to register FLAIR to T1? Thank?you, Edina _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://secure-web.cisco.com/1dS-NlFBksiulwBVJ54OgNH06JWJ8AG7AYE-cayHfJPVbT… -------------- next part -------------- An HTML attachment was scrubbed... URL: http://secure-web.cisco.com/15ur6zNJiUz9soStCFUyUoQOdvg5y4hQwXLe5X8AMjZJymz… ------------------------------ Message: 6 Date: Mon, 5 Apr 2021 09:48:22 -0400 From: "Douglas N. Greve" <dgreve(a)mgh.harvard.edu> Subject: Re: [Freesurfer] functional to anatomical registration question To: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <067c4ed5-b664-87a3-722b-45b9da81ab95(a)mgh.harvard.edu> Content-Type: text/plain; charset="windows-1252" You can add --aparc+aseg (hit 'c' to toggle on and off), alternatively You can use tkregsiterfv (same command arguments) but add -aparc+aseg -seg-outline You will need to use the lta registration file (not the .dat) On 3/29/2021 6:13 PM, Nasiriavanaki, Zahra wrote: Dear Freesurferers, I have a question and I appreciate it much if you could please reply. I need to know how to check *subcortical*?functional to anatomical registration. I know for checking the cortical registration I can use the below command: tkregister2 --s $subj --mov ?template.nii.gz ?--surf --reg init.register.dof6.dat Could you please tell me what command should I use to check the registration in subcortex? Thanks MOna *Zahra (Mona) Nasiriavanaki, M.D.* Postdoctoral Research Fellow Department of Psychiatry Massachusetts General?Hospital 149 13th Street, 149-2615 Boston, MA, USA, 02129 _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://secure-web.cisco.com/1dS-NlFBksiulwBVJ54OgNH06JWJ8AG7AYE-cayHfJPVbT… -------------- next part -------------- An HTML attachment was scrubbed... URL: http://secure-web.cisco.com/1y62Sj3thJpJWBg3qJo9fZaWBuUyrzHiAYeGC0AsnK4ixG-… ------------------------------ Message: 7 Date: Mon, 5 Apr 2021 09:49:45 -0400 From: "Douglas N. Greve" <dgreve(a)mgh.harvard.edu> Subject: Re: [Freesurfer] Problem with freesurfer measures To: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <70cde94b-a8f5-3504-72ca-bd43a4f9c384(a)mgh.harvard.edu> Content-Type: text/plain; charset="utf-8" What are your command lines? On 3/30/2021 5:24 AM, Alberto Del Cerro Leon wrote: ????????External Email - Use Caution Thanks a lot, It works!, now I have obtained values to ctx and wm volumes for each area. However when I look at the gray matter volume values calculated by mri_anatomical stats, the results are pretty similar to the ctx-ROIs calculated by mri_segstats, but not the same. It is normal? In that case what measure will be more suitable? El lun, 29 mar 2021 a las 5:22, Douglas N. Greve (<dgreve(a)mgh.harvard.edu <mailto:dgreve@mgh.harvard.edu>>) escribi?: ???You'll need to create your own color table by adding 3000 to the ???left hemi structures and 4000 to the right hemi structures. Look ???at the 3000s and 4000s in $FREESURFER_HOME/FreeSurferColorLUT.txt ???On 3/26/2021 10:09 AM, Alberto Del Cerro Leon wrote: ???????????External Email - Use Caution ???Hello Douglas, i tried but when i look at the wmparc.mgz created ???by the code >>mri_aparc2aseg --s 215 --labelwm --hypo-as-wm ???--rip-unknown --volmask --o mri/wmparc.mgz --annot myAAL it takes ???the index and the names from FreeSurferColorLUT instead of the ???names in the colorLUT associated?with myAAL.annot then the ROIs ???are disorganized. Could you help me with this problem? ???El jue, 25 mar 2021 a las 14:59, Douglas N. Greve ???(<dgreve(a)mgh.harvard.edu <mailto:dgreve@mgh.harvard.edu>>) escribi?: ???????Look in recon-all.log to find the command that creates the ???????wmparc.mgz. Run that command changing the aparc annot to your ???????annot and the output to a new file name. Look in ???????wmparc.stats; at the top will be an mri_segstats command ???????line. Copy that command line changing the file names as needed. ???????On 3/22/2021 9:06 AM, Alberto Del Cerro Leon wrote: ???????????????External Email - Use Caution ???????Thanks!, how can I obtain the white matter volume stats ???????using my annotation file? ???????El mar, 16 mar 2021 a las 16:59, Douglas N. Greve ???????(<dgreve(a)mgh.harvard.edu <mailto:dgreve@mgh.harvard.edu>>) ???????escribi?: ???????????I think they will give very similar results, but my ???????????guess is that #1 is a little better ???????????On 3/8/2021 11:40 AM, Alberto Del Cerro Leon wrote: ???????????????????External Email - Use Caution ???????????I want to use the annotation file created by myself in ???????????fsaverage to calculate the anatomical stats, but i ???????????dont?know what is the best workflow. ???????????1. Convert the annotation file to each subject space ???????????using mri_sur2surf and using mri_anatomical_stats in ???????????each subject ???????????2. Convert the surface of each subject to fsaverage ???????????space and use mri_segstats to obtain the data, in this ???????????case i dont?know what surface i have to convert to ???????????fsaverage space to do it (i can see thickness ???????????(lh/rh.thickness) and volume (lh/rh.volume) but not ???????????folding index and white matter volume) ???????????Any idea? ???????????El lun, 8 mar 2021 a las 16:04, Fischl, Bruce ???????????(<BFISCHL(a)mgh.harvard.edu ???????????<mailto:BFISCHL@mgh.harvard.edu>>) escribi?: ???????????????Hi Alberto ????????????????1. And 4. Are not properties of single surfaces ? ???????????????????they are computed from the white and the pial. ???????????????????For 2 and 3 that is really up to you ???????????????Cheers ???????????????Bruce ???????????????*From:* freesurfer-bounces(a)nmr.mgh.harvard.edu ???????????????<mailto:freesurfer-bounces@nmr.mgh.harvard.edu> ???????????????<freesurfer-bounces(a)nmr.mgh.harvard.edu ???????????????<mailto:freesurfer-bounces@nmr.mgh.harvard.edu>> ???????????????*On Behalf Of *Alberto Del Cerro Leon ???????????????*Sent:* Monday, March 8, 2021 7:02 AM ???????????????*To:* Freesurfer support list ???????????????<freesurfer(a)nmr.mgh.harvard.edu ???????????????<mailto:freesurfer@nmr.mgh.harvard.edu>> ???????????????*Subject:* [Freesurfer] Problem with freesurfer ???????????????measures ???????????????*????????External Email - Use Caution * ???????????????Hello Freesurfer team, I am using an annotation ???????????????file that i've created previously to obtain the ???????????????measures of some ROIs. To do that i am using de ???????????????commands mri_surf2surf and mri_segstats. I want to ???????????????obtain the following measures: ???????????????1. Gray and White Matter Volume ???????????????2. Folding Index ???????????????3. Curvature measures ???????????????4. Thickness ???????????????However I don't know what surface in the surf ???????????????folder of each subject I have to use. Could u help me? ???????????????_______________________________________________ ???????????????Freesurfer mailing list ???????????????Freesurfer(a)nmr.mgh.harvard.edu ???????????????<mailto:Freesurfer@nmr.mgh.harvard.edu> ???????????????*MailScanner has detected a possible fraud attempt ???????????????from "secure-web.cisco.com" claiming to be* ???????????????https://secure-web.cisco.com/1dS-NlFBksiulwBVJ54OgNH06JWJ8AG7AYE-cayHfJPVbTKex0CQR6WnJqjC8JoIzm7_eMdZsL6Y54UFodC6LZcy4JWJg5_k7FoHtCpK14QFsSMWuVml81c-ZC6szy6iUl8iYVNKOahK3dZIeSvKyXtN9O0bUmOror7aJKZGwA75UZPrkLIbJDp0-twu0MLfoiBoBPN4BcSKoeS8xmCAzARi21Cp7P_Z1EOAQOd01fJm_cNqXdC3vohizq8JwmgScCHN3G2rnnVhQ_zkLnFRdlA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer ???????????????<https://secure-web.cisco.com/1YJFf9_v-FCEIEML34ObuC19lwndNnPr3qXQ27W-KJa3aD…> ???????????_______________________________________________ ???????????Freesurfer mailing list ???????????Freesurfer(a)nmr.mgh.harvard.edu 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???https://secure-web.cisco.com/1dS-NlFBksiulwBVJ54OgNH06JWJ8AG7AYE-cayHfJPVbTKex0CQR6WnJqjC8JoIzm7_eMdZsL6Y54UFodC6LZcy4JWJg5_k7FoHtCpK14QFsSMWuVml81c-ZC6szy6iUl8iYVNKOahK3dZIeSvKyXtN9O0bUmOror7aJKZGwA75UZPrkLIbJDp0-twu0MLfoiBoBPN4BcSKoeS8xmCAzARi21Cp7P_Z1EOAQOd01fJm_cNqXdC3vohizq8JwmgScCHN3G2rnnVhQ_zkLnFRdlA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer ???<https://secure-web.cisco.com/1wwKasfUxceW84pkucUGkmsYQ_veBEUDGdn4KBJ5uoTfR9…> _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://secure-web.cisco.com/1dS-NlFBksiulwBVJ54OgNH06JWJ8AG7AYE-cayHfJPVbT… -------------- next part -------------- An HTML attachment was scrubbed... URL: http://secure-web.cisco.com/1qA8IdWW5xZovcBpPlksl2cD8nlLvPNcVgqS0hJT1mTUSyq… ------------------------------ Message: 8 Date: Mon, 5 Apr 2021 09:51:34 -0400 From: "Douglas N. Greve" <dgreve(a)mgh.harvard.edu> Subject: Re: [Freesurfer] ERROR: Cannot find stats file To: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <5220512d-4f0c-44e3-63a3-3c2c5e3f4894(a)mgh.harvard.edu> Content-Type: text/plain; charset="windows-1254" Does that file exist? If not, have you run the amygdalar nuclei segmentation? On 3/30/2021 3:00 PM, atacan zeybek wrote: ????????External Email - Use Caution ????????External Email - Use Caution Hello FreeSurfer Developers, I'm attempting to create a text file of amygdalar nuclei of given subjects. I use this command: asegstats2table --subjects 8070? 8071? 8077 --statsfile=amygdalar-nuclei.lh.T1.v21.stats --tablefile=amygdalarnuclei.lh.T1.v21.txt ?skip And get an error like this: ERROR: Cannot find stats file /home/atacan/Desktop/freesurfer/subjects/8070/stats/amygdalar-nuclei.lh.T1.v21.stats Unfortunately I can't search the mail archives because I get an another error while loading the page. Freesurfer version: CentOS 7 x86_64 (64b) tar archive Platform: Ubuntu 20.04.2 LTS _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://secure-web.cisco.com/1f3lJRMHRomDlVaLdu7jT-2gE1_o06hzLNIomCGjpe9xt6… -------------- next part -------------- An HTML attachment was scrubbed... URL: http://secure-web.cisco.com/1Xs7o1VHT4tsIEzaai20pMytv6BaTDMT6HS4GMtc_fS8_2k… ------------------------------ Message: 9 Date: Mon, 5 Apr 2021 09:54:24 -0400 From: "Douglas N. Greve" <dgreve(a)mgh.harvard.edu> Subject: Re: [Freesurfer] Subthalamic nucleus volume To: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <2737d6a7-618b-cd97-b4a2-fe29f4c1ce49(a)mgh.harvard.edu> Content-Type: text/plain; charset="utf-8" If you want the volume in the native space, then why not just register your volume to mni space, then map the label back to the individual? You could probably do that all with FSL (or SPM). BTW, the "volume" you get is not at all likely to be accurate. It will just reflect the registration in that area. On 3/30/2021 4:28 PM, T. Pansuwan wrote: ????????External Email - Use Caution ????????External Email - Use Caution Dear Freesurfer experts, As part of my project, I would need to have subthalamic nucleus as one of my ROIs in which this is not available by Freesurfer. I found a probabilistic subthalamic nucleus atlas in FSL atlases (in MNI152 space) and thought I would convert this to fsaverage space. I have attempted: mri_label2vol ?reg $FREESURFER_HOME/average/mni152.register.dat ?seg STN-maxprob-thr25-0.5mm.nii.gz ?temp $FREESURFER_HOME/subjects/fsaverage/mri/orig.mgz ?o STN_mni152_in_mni305.nii.gz But the location was much more dorsal than original, 1) I was wondering if there are alternative methods I should try and what could have been the problem? At the end, I hope to obtain individual subject?s subthalamic nucleus volume, 2) I was wondering how to convert volume in fsaverage space to labels in fsaverage space so that I can convert the labels to native space? Thank you so much! Tanrada Pansuwan _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://secure-web.cisco.com/1ppqWMizlh4d_5aHnRxC-N7xDWoDNlu2fkpAR06UT5xuYH… -------------- next part -------------- An HTML attachment was scrubbed... URL: http://secure-web.cisco.com/1CwoCDJPcUN3HzWIa_tMvNbhKgwAR5wF28gBD4sNxUtbIqM… ------------------------------ Message: 10 Date: Mon, 5 Apr 2021 09:56:13 -0400 From: "Douglas N. Greve" <dgreve(a)mgh.harvard.edu> Subject: Re: [Freesurfer] Talairach Failed: Distorted T1 To: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <6037d9f2-eadc-f756-db09-01ef43e60f2f(a)mgh.harvard.edu> Content-Type: text/plain; charset="windows-1252" Correct. You can measure the volume of the brainstem and add it on. Eg, mri_segstats --ctab-default --seg aseg.mgz --id 16 --sum brainstem.dat On 3/30/2021 7:03 PM, Harkey, Thomas Jarrott wrote: ????????External Email - Use Caution Douglas, Thank you for your help. Another question. The FreeSurfer wiki states that for version 5.2 and later, the brainstem is not included in the global measures of volume because the amount of brainstem changes depending upon the field of view of the volume acquisition. We are interested in the obtaining the volume of the entire brain using the BrainVolNotVent value. Does this mean that BrainVolNotVent does not include the brainstem and therefore underestimates total brain volume? Is there a way to correct for this? Kind regards, Thomas Harkey UAMS College of Medicine M3 ------------------------------------------------------------------------ *From:* freesurfer-bounces(a)nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Douglas N. Greve <dgreve(a)mgh.harvard.edu> *Sent:* Thursday, March 25, 2021 9:48 PM *To:* freesurfer(a)nmr.mgh.harvard.edu <freesurfer(a)nmr.mgh.harvard.edu> *Subject:* Re: [Freesurfer] Talairach Failed: Distorted T1 That is an axial scan that only covers 25mm of the brain inferior-superior. This is not whole brain coverage, which is causing the problem On 3/25/2021 9:07 PM, Harkey, Thomas Jarrott wrote: ????????External Email - Use Caution Douglas, Thank you for your help. I have pasted the result below. Volume information for 2020-24axialScalarvolumeall/mri/orig/001.mgz ? ? ? ? ? type: MGH ? ? dimensions: 384 x 384 x 25 ? ?voxel sizes: 0.598958, 0.598958, 1.000000 ? ? ? ? ? type: SHORT (4) ? ? ? ? ? ?fov: 230.000 ? ? ? ? ? ?dof: 1 ? ? ? ? xstart: -115.0, xend: 115.0 ? ? ? ? ystart: -115.0, yend: 115.0 ? ? ? ? zstart: -12.5, zend: 12.5 ? ? ? ? ? ? TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees ? ? ? ?nframes: 1 ? ? ? ?PhEncDir: UNKNOWN ? ? ? ?FieldStrength: 0.000000 ras xform present ? ? xform info: x_r = ?-0.9841, y_r = ?-0.0087, z_r = ?-0.1777, c_r = ? ?15.3722 ? ? ? ? ? ? ? : x_a = ? 0.0272, y_a = ?-0.9944, z_a = ?-0.1022, c_a = ? ?14.0701 ? ? ? ? ? ? ? : x_s = ?-0.1758, y_s = ?-0.1054, z_s = 0.9788, c_s = ? -75.3479 talairach xfm : Orientation ? : LPS Primary Slice Direction: axial voxel to ras transform: ? ? ? ? ? ? ? ?-0.5894 ?-0.0052 ?-0.1777 ? 131.7540 ? ? ? ? ? ? ? ? 0.0163 ?-0.5956 ?-0.1022 ? 126.5760 ? ? ? ? ? ? ? ?-0.1053 ?-0.0631 ? 0.9788 ? -55.2497 ? ? ? ? ? ? ? ? 0.0000 ? 0.0000 ? 0.0000 ? ? 1.0000 voxel-to-ras determinant 0.358751 ras to voxel transform: ? ? ? ? ? ? ? ?-1.6429 ? 0.0454 ?-0.2935 ? 194.5030 ? ? ? ? ? ? ? ?-0.0144 ?-1.6602 ?-0.1759 ? 202.3262 ? ? ? ? ? ? ? ?-0.1777 ?-0.1022 ? 0.9788 ? ?90.4171 ? ? ? ? ? ? ? ? 0.0000 ? 0.0000 ? 0.0000 ? ? 1.0000 Kindly, Thomas Harkey UAMS College of Medicine class of 2022 ------------------------------------------------------------------------ *From:* freesurfer-bounces(a)nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> <freesurfer-bounces(a)nmr.mgh.harvard.edu> <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve <dgreve(a)mgh.harvard.edu> <mailto:dgreve@mgh.harvard.edu> *Sent:* Thursday, March 25, 2021 9:11 AM *To:* freesurfer(a)nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> <freesurfer(a)nmr.mgh.harvard.edu> <mailto:freesurfer@nmr.mgh.harvard.edu> *Subject:* Re: [Freesurfer] Talairach Failed: Distorted T1 It looks like something is wrong with your input. For starters, the voxel size looks huge. Run mri_info subject/mri/orig/001.mgz and send the result On 3/23/2021 10:54 PM, Harkey, Thomas Jarrott wrote: ????????External Email - Use Caution Hello, My name is Thomas Harkey and I am conducting research using FreeSurfer. After running recon-all on this patient, the Talairach failed according to the .log file. No stats were calculated but loading the orig.mgz file into FreeView looks like this (see image attached). This DICOM file was successfully uploaded into other programs. How can I fix this error? Kind regards, -- *Thomas Harkey ** University of Arkansas for Medical Sciences*** *College of Medicine, Class of 2022 501-553-6318* *TJHarkey(a)uams.edu <mailto:TJHarkey@uams.edu>* ------------------------------------------------------------------------ Confidentiality Notice: This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply e-mail and destroy all copies of the original message. _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu ?<mailto:Freesurfer@nmr.mgh.harvard.edu> *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1dS-NlFBksiulwBVJ54OgNH06JWJ8AG7AYE-cayHfJPVbT… ?<https://secure-web.cisco.com/1FinEQl6RRfucQGlK5MSVfPvjTbxU_EPXx-8LVu7Oz8rye… MfZ-2DoN8R6xJFbHeLbIOeuCDm-5FBNtoxxmTiPk-2526m-253Df-5FhRKBl8FfYqItx-5FYTHvwSb0eK7xmVStu8OohcmGpv4-2526s-253DLmMgJVLtfQOHq2emGDgbFJVWNymeVRGFjJmt6z53LdY-2526e-253D%26d%3DDwMD-g%26c%3D27AKQ-AFTMvLXtgZ7shZqsfSXu-Fwzpqk4BoASshREk%26r%3Dlni-DQNMfZ-oN8R6xJFbHeLbIOeuCDm_BNtoxxmTiPk%26m%3DawJnlMygdhBegQ_WVfcDMfdH55wc4KvX3PUeL4tsawc%26s%3D3zERWJJILBCAjKwzQVMXBEDDoJn75mLwiFCawoehuDk%26e%3D> _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu ?<mailto:Freesurfer@nmr.mgh.harvard.edu> *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1dS-NlFBksiulwBVJ54OgNH06JWJ8AG7AYE-cayHfJPVbT… ?<https://secure-web.cisco.com/1sxKYDyFUn1L-DRql-3YoGcdi9SZ0u-IIBFf8WTifb71AH…> _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://secure-web.cisco.com/1dS-NlFBksiulwBVJ54OgNH06JWJ8AG7AYE-cayHfJPVbT… -------------- next part -------------- An HTML attachment was scrubbed... URL: http://secure-web.cisco.com/1yMm___muWNZHQR1OB_lBJOOKKV17x_h_lK0YyNArocRJO6… ------------------------------ Message: 11 Date: Mon, 5 Apr 2021 09:57:27 -0400 From: "Douglas N. Greve" <dgreve(a)mgh.harvard.edu> Subject: Re: [Freesurfer] quantification of volume of perivascular spaces To: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <183d083f-5146-90e2-85c1-5b58d7526c30(a)mgh.harvard.edu> Content-Type: text/plain; charset="utf-8" It might work, but I doubt it has been tested. On 3/31/2021 5:54 AM, Anton?n ?koch wrote: ????????External Email - Use Caution Dear experts, We would like to quantify volume of brain perivascular spaces. Ideally longitudinally - i.e. to study the dynamics of perivascular spaces in multiple measurement of the same subject. Is it possible to use samseg for this? Do you think, that --lesion flag in samseg would work estimation of perivascular spaces? Or other setting of samseg will be better option? Or, would you rather recommend other tools? Any idea/comment will be greatly appreciated. Regards, Antonin Skoch _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://secure-web.cisco.com/1dS-NlFBksiulwBVJ54OgNH06JWJ8AG7AYE-cayHfJPVbT… -------------- next part -------------- An HTML attachment was scrubbed... URL: http://secure-web.cisco.com/1OmE17zGs7UfXRCaGfdz-ASFfyoXEqrFwqZzpl5pCPNMFah… ------------------------------ Message: 12 Date: Mon, 5 Apr 2021 15:41:22 +0000 From: "Cook, Philip" <cookpa(a)pennmedicine.upenn.edu> Subject: [Freesurfer] "ERROR: crypt() returned null with 4-line file" To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <BL0PR04MB5028D2F00940DA4CE992E424E67A9(a)BL0PR04MB5028.namprd04.prod.outlook.com> Content-Type: text/plain; charset="us-ascii" ???????External Email - Use Caution Dear FreeSurfer developers, I have also encountered the error that Katja Zoner reported in https://secure-web.cisco.com/1HqVP4_2gCSsHuuEFWzIN0yTWdDhhIeKNpc8cqD9BfBOmm… We work on different servers within the same institution and have been in contact with our administrators, we are sure at this point that the error is caused by FIPS 140 compliance on some of our systems. It is unrelated to Singularity. The crypt() function, as called in freesurfer/utils/chklc.cpp, returns NULL with errno == EPERM on machines booted in FIPS mode. I believe these users have encountered the same problem https://secure-web.cisco.com/1-z_qWpPYjwD6UccsUQP4XQEVo4YMH5WkF2I0eRZ2Z2G-7… https://secure-web.cisco.com/1D8Zt97JISxcqWsV-6sX9O6GUs5X59E2NOYaxNQqkDBr8t… As one of the above users noted, certain institutions (such as the Veterans Administration) require FIPS mode, as do studies using sensitive data. Our administrators have agreed to provide some "insecure" machines to run FreeSurfer binaries and containers for the time being, but we're concerned about the sustainability of this longer term. I think the issue could be resolved by using a FIPS-compliant algorithm in the call to crypt(). For example, I've tested crypt() with the SHA-512 algorithm in FIPS mode, and this works ?crypt_gkey = crypt(gkey, "$6$FS"); but this would require the license file to contain an SHA-512 encrypted gkey in addition to the DES one that currently exists. Alternatively, we can check if errno == EPERM after the call to crypt(), and bypass the encryption check in that case. I understand that these solutions are non-trivial and could raise backwards compatibility or license compliance issues. Unfortunately, I've not been able to find any other workaround. Thanks -------------- next part -------------- An HTML attachment was scrubbed... URL: http://secure-web.cisco.com/1hQO8aio1iYZsDQjPx_hPnREmKeykrWCbxRKLIaHud61YRh… ------------------------------ Message: 13 Date: Mon, 5 Apr 2021 17:47:03 +0200 From: Alberto Del Cerro Leon <bertocerron(a)gmail.com> Subject: Re: [Freesurfer] Problem with freesurfer measures To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <CAKXUO47yYhA=k9JK9dbfr_q05dz=1d+nznp-TT8dSaiTmZkD6A(a)mail.gmail.com> Content-Type: text/plain; charset="utf-8" ???????External Email - Use Caution To obtain de stats from mri_anatomical stats i used *>>mris_anatomical_stats -a /usr/local/freesurfer/subjects/218/label/rh.myAAL.annot -f* */usr/local/freesurfer/subjects/218/stats/rh.myAAL.stats -b 218 rh* In another hand, the workflow to obatian the stats from mri_segstats was: *mri_aparc2aseg --s 218 --labelwm --hypo-as-wm --rip-unknown --volmask --o /usr/local/freesurfer/subjects/218/mri/wmmyAAL.mgz **--annot myAAL* *>>**mri_segstats --seg /usr/local/freesurfer/subjects/218/mri/wmmyAAL.mgz* *--ctab /home/neuroimage/fsl/FreeSurfer/wmAALColorLUT.txt --sum /usr/local/freesurfer/subjects/218/stats/wmmyAAL.stats * *-**-pv /usr/local/freesurfer/subjects/218/mri/norm.mgz --excludeid 0 --brainmask /usr/local/freesurfer/subjects/218/mri/brainmask.mgz --in /usr/local/freesurfer/subjects/218/mri/norm.mgz* *--in-intensity-name norm --in-intensity-units MR --subject 218 --surf-wm-vol --etiv* El lun, 5 abr 2021 a las 15:50, Douglas N. Greve (<dgreve(a)mgh.harvard.edu>) escribi?: What are your command lines? On 3/30/2021 5:24 AM, Alberto Del Cerro Leon wrote: ???????External Email - Use Caution Thanks a lot, It works!, now I have obtained values to ctx and wm volumes for each area. However when I look at the gray matter volume values calculated by mri_anatomical stats, the results are pretty similar to the ctx-ROIs calculated by mri_segstats, but not the same. It is normal? In that case what measure will be more suitable? El lun, 29 mar 2021 a las 5:22, Douglas N. Greve (<dgreve(a)mgh.harvard.edu>) escribi?: You'll need to create your own color table by adding 3000 to the left hemi structures and 4000 to the right hemi structures. Look at the 3000s and 4000s in $FREESURFER_HOME/FreeSurferColorLUT.txt On 3/26/2021 10:09 AM, Alberto Del Cerro Leon wrote: ???????External Email - Use Caution Hello Douglas, i tried but when i look at the wmparc.mgz created by the code >>mri_aparc2aseg --s 215 --labelwm --hypo-as-wm --rip-unknown --volmask --o mri/wmparc.mgz --annot myAAL it takes the index and the names from FreeSurferColorLUT instead of the names in the colorLUT associated with myAAL.annot then the ROIs are disorganized. Could you help me with this problem? El jue, 25 mar 2021 a las 14:59, Douglas N. Greve (< dgreve(a)mgh.harvard.edu>) escribi?: Look in recon-all.log to find the command that creates the wmparc.mgz. Run that command changing the aparc annot to your annot and the output to a new file name. Look in wmparc.stats; at the top will be an mri_segstats command line. Copy that command line changing the file names as needed. On 3/22/2021 9:06 AM, Alberto Del Cerro Leon wrote: ???????External Email - Use Caution Thanks!, how can I obtain the white matter volume stats using my annotation file? El mar, 16 mar 2021 a las 16:59, Douglas N. Greve (< dgreve(a)mgh.harvard.edu>) escribi?: I think they will give very similar results, but my guess is that #1 is a little better On 3/8/2021 11:40 AM, Alberto Del Cerro Leon wrote: ???????External Email - Use Caution I want to use the annotation file created by myself in fsaverage to calculate the anatomical stats, but i dont know what is the best workflow. 1. Convert the annotation file to each subject space using mri_sur2surf and using mri_anatomical_stats in each subject 2. Convert the surface of each subject to fsaverage space and use mri_segstats to obtain the data, in this case i dont know what surface i have to convert to fsaverage space to do it (i can see thickness (lh/rh.thickness) and volume (lh/rh.volume) but not folding index and white matter volume) Any idea? El lun, 8 mar 2021 a las 16:04, Fischl, Bruce (<BFISCHL(a)mgh.harvard.edu>) escribi?: Hi Alberto ??1. And 4. Are not properties of single surfaces ? they are ??computed from the white and the pial. For 2 and 3 that is really up to you Cheers Bruce *From:* freesurfer-bounces(a)nmr.mgh.harvard.edu < freesurfer-bounces(a)nmr.mgh.harvard.edu> *On Behalf Of *Alberto Del Cerro Leon *Sent:* Monday, March 8, 2021 7:02 AM *To:* Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> *Subject:* [Freesurfer] Problem with freesurfer measures * ???????External Email - Use Caution ???????* Hello Freesurfer team, I am using an annotation file that i've created previously to obtain the measures of some ROIs. To do that i am using de commands mri_surf2surf and mri_segstats. I want to obtain the following measures: 1. Gray and White Matter Volume 2. Folding Index 3. Curvature measures 4. Thickness However I don't know what surface in the surf folder of each subject I have to use. Could u help me? _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1ig2ol_YfPL7vkGsCqXX1xseLR5cg4PLQwrszsbYhNdPL0… <https://secure-web.cisco.com/1YJFf9_v-FCEIEML34ObuC19lwndNnPr3qXQ27W-KJa3aD…> _______________________________________________ Freesurfer mailing listFreesurfer(a)nmr.mgh.harvard.edu*MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1ig2ol_YfPL7vkGsCqXX1xseLR5cg4PLQwrszsbYhNdPL0… <https://secure-web.cisco.com/1G_h97ZZmS1M3Mu1WvIxpTpCamKUMZrdeii7Mb-_WyhLnq…> _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1ig2ol_YfPL7vkGsCqXX1xseLR5cg4PLQwrszsbYhNdPL0… <https://secure-web.cisco.com/1G_h97ZZmS1M3Mu1WvIxpTpCamKUMZrdeii7Mb-_WyhLnq…> _______________________________________________ Freesurfer mailing listFreesurfer(a)nmr.mgh.harvard.edu*MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1xoPMQAneRNhi_EotQOagMUtvb1b6JAtMOD6p63fHLkJfc… <https://secure-web.cisco.com/1ekuMRUoFakA2GcA-HAYdzP-YJXE02k2qNXi0TJVuyogwG…> _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1xoPMQAneRNhi_EotQOagMUtvb1b6JAtMOD6p63fHLkJfc… <https://secure-web.cisco.com/1ekuMRUoFakA2GcA-HAYdzP-YJXE02k2qNXi0TJVuyogwG…> _______________________________________________ Freesurfer mailing listFreesurfer(a)nmr.mgh.harvard.edu*MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1xoPMQAneRNhi_EotQOagMUtvb1b6JAtMOD6p63fHLkJfc… <https://secure-web.cisco.com/1wwKasfUxceW84pkucUGkmsYQ_veBEUDGdn4KBJ5uoTfR9…> _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1xoPMQAneRNhi_EotQOagMUtvb1b6JAtMOD6p63fHLkJfc… <https://secure-web.cisco.com/1wwKasfUxceW84pkucUGkmsYQ_veBEUDGdn4KBJ5uoTfR9…> _______________________________________________ Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://secure-web.cisco.com/1xoPMQAneRNhi_EotQOagMUtvb1b6JAtMOD6p63fHLkJfc… -------------- next part -------------- An HTML attachment was scrubbed... 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10 May '21

External Email - Use Caution Dear All, Due to my study, I have been unsuccessfully trying to co-register the hippocampal and amygdala segmented file (obtained from segmentHA_T2.sh) to my T1-weighted anatomical image (.nii), so that I can use the segmented file as a mask for later ROI analysis. However, despite trying in several ways with mri_robust_register and tkregister2, I have not been able to coregister the 2 together. Any suggestions? Kind regards, Greg s1034199

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