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gray matter volume of the entorhinal cortex
by Laboratorio de Neurociencia Funcional 04 Feb '19

04 Feb '19

External Email - Use Caution Dear Freesurfers, gray matter volume of the entorhinal cortex (EC) can be obtained either in the ?h.aparc.stats or ?h.BA_exvivo.stats/?h.BA_exvivo.thresh.stats files. Considering that all our T1 images were manually edited on a slice-by-slice basis to correct pial surface misplacements and erroneous white matter segmentation, which volume measure of the EC would be more precise? I assume that gray matter volume contained in ?h.BA_exvivo.thresh.stats were thresholded at a specific probability value (% of case overlapping). Which probability value was used? Is there a reference paper explaining how probabilistic maps of EC were built based on ex vivo MRI contrast? Thank you in advance. Best, Jose L. Cantero

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Re: [Freesurfer] Surface to Volume conversion
by Bunting, Emma 04 Feb '19

04 Feb '19

External Email - Use Caution Hi Bruce, I ran the mri_info command on the sig.mgh and the sig.lh.nii.gz files for participant 124 and got these outputs... For sig.mgh: Volume information for sig.mgh type: MGH dimensions: 163842 x 1 x 1 voxel sizes: 1.000000, 1.000000, 1.000000 type: FLOAT (3) fov: 163842.000 dof: 0 xstart: -81921.0, xend: 81921.0 ystart: -0.5, yend: 0.5 zstart: -0.5, zend: 0.5 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 = -1.0000, y_r = 0.0000, z_r = 0.0000, c_r = 0.0000 : x_a = 0.0000, y_a = 0.0000, z_a = 1.0000, c_a = 0.0000 : x_s = 0.0000, y_s = -1.0000, z_s = 0.0000, c_s = 0.0000 talairach xfm : Orientation : LIA Primary Slice Direction: coronal voxel to ras transform: -1.0000 0.0000 0.0000 81921.0000 0.0000 0.0000 1.0000 -0.5000 0.0000 -1.0000 0.0000 0.5000 0.0000 0.0000 0.0000 1.0000 voxel-to-ras determinant -1 ras to voxel transform: -1.0000 -0.0000 -0.0000 81921.0000 -0.0000 -0.0000 -1.0000 0.5000 -0.0000 1.0000 -0.0000 0.5000 -0.0000 -0.0000 -0.0000 1.0000 For sig.lh.nii.gz: Volume information for sig.lh.nii.gz type: nii dimensions: 163842 x 1 x 1 voxel sizes: 1.000000, 1.000000, 1.000000 type: FLOAT (3) fov: 163842.000 dof: 0 xstart: -81921.0, xend: 81921.0 ystart: -0.5, yend: 0.5 zstart: -0.5, zend: 0.5 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 = -1.0000, y_r = 0.0000, z_r = 0.0000, c_r = -68267.5000 : x_a = 0.0000, y_a = 0.0000, z_a = 1.0000, c_a = -2.5000 : x_s = 0.0000, y_s = -1.0000, z_s = 0.0000, c_s = 0.0000 Orientation : LIA Primary Slice Direction: coronal voxel to ras transform: -1.0000 0.0000 0.0000 13653.5000 0.0000 0.0000 1.0000 -3.0000 0.0000 -1.0000 0.0000 0.5000 0.0000 0.0000 0.0000 1.0000 voxel-to-ras determinant -1 ras to voxel transform: -1.0000 -0.0000 -0.0000 13653.5000 -0.0000 -0.0000 -1.0000 0.5000 -0.0000 1.0000 -0.0000 3.0000 -0.0000 -0.0000 -0.0000 1.0000 Please let me know if you need any other information in order to help with our problem, Best wishes, Emma ________________________________ 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: 25 January 2019 17:00 To: freesurfer(a)nmr.mgh.harvard.edu Subject: Freesurfer Digest, Vol 179, Issue 41 Send Freesurfer mailing list submissions to freesurfer(a)nmr.mgh.harvard.edu To subscribe or unsubscribe via the World Wide Web, visit https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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: Longitudinal processing with windows subsystem for linux (WSL) using ubuntu 18.04.1 LTS (Hoopes, Andrew) 2. Re: FSFAST poor registration (Greve, Douglas N.,Ph.D.) 3. Re: Surface to volume conversion (Bruce Fischl) 4. Re: Functional connectivty walkthrough step 8 error (Greve, Douglas N.,Ph.D.) 5. Re: cortical thickness calculation based on hammersmith segmentation (Greve, Douglas N.,Ph.D.) 6. Re: FSFAST poor registration (Keri Woods) 7. Re: Functional connectivty walkthrough step 8 error (Amrita Bedi) 8. Re: Orientation by direction cosines (Greve, Douglas N.,Ph.D.) 9. Re: Functional connectivty walkthrough step 8 error (Amrita Bedi) 10. Re: Functional connectivty walkthrough step 8 error (Amrita Bedi) 11. Re: Functional connectivty walkthrough step 8 error (Greve, Douglas N.,Ph.D.) ---------------------------------------------------------------------- Message: 1 Date: Fri, 25 Jan 2019 16:24:14 +0000 From: "Hoopes, Andrew" <AHOOPES(a)mgh.harvard.edu> Subject: Re: [Freesurfer] Longitudinal processing with windows subsystem for linux (WSL) using ubuntu 18.04.1 LTS To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <2A2251F1-6E66-4125-9A96-76700348245B(a)mgh.harvard.edu> Content-Type: text/plain; charset="utf-8" I believe this python2 issue has been fixed in the dev version found here https://raw.githubusercontent.com/freesurfer/freesurfer/dev/scripts/long_mr… best, Andrew ?On 1/25/19, 10:08 AM, "freesurfer-bounces(a)nmr.mgh.harvard.edu on behalf of Bruce Fischl" <freesurfer-bounces(a)nmr.mgh.harvard.edu on behalf of fischl(a)nmr.mgh.harvard.edu> wrote: Hi Falk thanks for catching the typo. I fixed it - nice to have an easy thing to fix for a change :) Bruce On Fri, 25 Jan 2019, falk.luesebrink(a)med.ovgu.de wrote: > > External Email - Use Caution > > Dear Juergen, > > > > Thanks for your quick reply! Actually the spelling error is in the error message. Taken from > http://martinos.org/~mreuter/long/long_mris_slopes > > > > # extensive error checks > > # if options.fsgd is None and > > if options.qdec is None: > > # print 'ERROR: Specify --fsgd or --qedc' > > parser.print_help() > > print '\nERROR: Specify --qedc (and other required arguments)\n' > > sys.exit(1) > > > > # if options.fsgd is not None and options.qdec is not None: > > # print 'ERROR: Specify either --fsgd or --qedc, not both' > > # sys.exit(1) > > > > At least Martin is consistent with his typo. :D > > > > Best, > > Falk > > > > Von: freesurfer-bounces(a)nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> Im Auftrag von Juergen Haenggi > Gesendet: Freitag, 25. Januar 2019 10:35 > An: Freesurfer Mailinglist <freesurfer(a)nmr.mgh.harvard.edu> > Betreff: Re: [Freesurfer] Longitudinal processing with windows subsystem for linux (WSL) using ubuntu 18.04.1 LTS > > > > External Email - Use Caution > > Dear Falk > > > > I have no idea, but recognised that the error refers to --qedc and not to --qdec. > > maybe there is a spelling error somewhere that is related to your problem. > > > > HTH > > Cheers > > J?rgen > > ----------------------------------------------------------------------------------------------------- > > University of Zurich > > Dr. J?rgen H?nggi, Ph.D. > > Department of Psychology > > Division Neuropsychology > > Binzmuehlestrasse 14, PO Box 25 > > 8050 Zurich, Switzerland > > > > 0041 44 635 73 97 (phone office) > > 0041 76 445 86 84 (phone mobile) > > 0041 44 635 74 09 (fax office) > > BIN 4.D.04 (office room number) > > > > j.haenggi(a)psychologie.uzh.ch (email) > > http://www.psychologie.uzh.ch/neuropsy/ (website) > > http://www.juergenhaenggi.ch (private website) > > > > This email (and any attachment/s) contains confidential and/or privileged > > information. If you are not the intended recipient (or have received this > > email in error) please notify the sender immediately and destroy this > > email. Any unauthorised copying, disclosure or distribution of the > > material in this email is strictly forbidden. > > ----------------------------------------------------------------------------------------------------- > > > > > > > > On 25 Jan 2019, at 10:26, falk.luesebrink(a)med.ovgu.de wrote: > > > > External Email - Use Caution > > > > Dear all, > > > > Has anyone run the longitudinal pipeline successfully using the WSL? I?m running it with Ubuntu 18.04.1 LTS > and freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c. > > > > I?m trying to process my first longitudinal data set following the instructions of the tutorial as close as > possible. The data has been processed without issues and now I want to do the statistical analysis. When I > run: > > long_mris_slopes --qdec ./long.qdec.table.dat --meas thickness --hemi lh --do-avg --do-rate --do-pc1 --do-spc > --do-stack --do-label --time years --qcache fsaverage --sd $SUBJECTS_DIR > > > > I get the following error: > > File "/home/luesebri/Software/FreeSurfer/bin/long_mris_slopes", line 448 > > print '\nERROR: Specify --qedc (and other required arguments)\n' > > ^ > > SyntaxError: invalid syntax > > > > I get comparable errors for any other long_* command I try to run, e.g. long_qdec_table with or without any > arguments gives: > > File "/home/luesebri/Software/FreeSurfer/bin/long_qdec_table", line 119 > > print '\nERROR: Specify --qedc' > > ^ > > SyntaxError: Missing parentheses in call to 'print'. Did you mean print('\nERROR: Specify --qedc')? > > > > Does anyone have a clue where this error originates from using either WSL or Ubuntu 18.04? > > > > Best, > > Falk > > ............................................... > > > > <image001.gif> > > Universit?tsklinik f?r Neurologie > > > > Otto-von-Guericke-Universit?t Magdeburg > Medizinische Fakult?t > Leipziger Str. 44 > 39120 Magdeburg > > > > Telefon: +49-391-6117-512 > > falk.luesebrink(a)med.ovgu.de > http://www.kneu.ovgu.de/kneu.html > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > ------------------------------ Message: 2 Date: Fri, 25 Jan 2019 16:34:14 +0000 From: "Greve, Douglas N.,Ph.D." <DGREVE(a)mgh.harvard.edu> Subject: Re: [Freesurfer] FSFAST poor registration To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <367a8e86-05d2-f02b-d19b-94401864c91d(a)mgh.harvard.edu> Content-Type: text/plain; charset="utf-8" Yes, that file is the only thing linking the functional to the anatomical. It's too bad you messed up the files, but I'm relieved it was not my software:). On 1/25/19 5:09 AM, Keri Woods wrote: External Email - Use Caution Hi Douglas Thanks very much for getting back to me. I created new separate directories and re-processed one of the problem subjects individually, and the registration worked well. So the problem is that the anatomical and functional images come from different subjects. But I've checked and the subjectname files are correct. That's the only thing linking the anatomical and functional images? Thanks very much, you've helped me a lot. Now I just have to go and see where I mixed up the files! Thanks again, Keri On Thu, Jan 24, 2019 at 10:32 PM Greve, Douglas N.,Ph.D. <DGREVE(a)mgh.harvard.edu<mailto:DGREVE@mgh.harvard.edu>> wrote: Can you tar up the anatomical and functional analyses and send them to me through our filedrop? https://gate.nmr.mgh.harvard.edu/filedrop2/ when it asks for an email of the recipient, use greve(a)nmr.mgh.harvard.edu<mailto:greve@nmr.mgh.harvard.edu> On 1/23/19 5:57 AM, Keri Woods wrote: > > External Email - Use Caution > > I meant some are nearly perfect. > > On Wed, Jan 23, 2019 at 11:49 AM Keri Woods <keri.woods(a)gmail.com<mailto:keri.woods@gmail.com> > <mailto:keri.woods@gmail.com<mailto:keri.woods@gmail.com>>> wrote: > > Hi Douglas > > Thanks for the response. > > No, some of the registrations are fine. Some are close, but not > perfect, while others are very bad. > > I've checked the subjectname file for some subjects with poor > registration (eg 20_101), and they are correct. > > Thanks, > Keri > > On Tue, Jan 22, 2019 at 8:57 PM Greve, Douglas N.,Ph.D. > <DGREVE(a)mgh.harvard.edu<mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu<mailto:DGREVE@mgh.harvard.edu>>> wrote: > > Are you saying that all of them have bad registrations? Some > of them > (eg, 20_1, 20_10) look like they should be good. Others (eg, > 20_101) > look like they could be bad. For the bad ones, are you totally > sure that > the subjetname file has the correct name of the subject? > > On 1/21/19 3:19 AM, Keri Woods wrote: > > > > External Email - Use Caution > > > > Hi Douglas > > > > Thank you for your reply. > > > > I'm using > freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.1-f53a55a > > > > I am using whole brain data. The functional and structural > images were > > acquired in different sessions on the same day, I don't know > if that > > complicated things? Each subject has 2 runs of the same task. > > > > This is what I get after running the command in the format of > > tkregister-sess -s sess01 -s sess02 -s sess03 -fsd bold > -per-run -bbr-sum > > > > 20_1 013 0.5155 > > 20_1 014 0.5090 > > 20_10 013 0.5247 > > 20_10 014 0.5229 > > 20_100 038 0.8420 > > 20_100 040 0.8443 > > 20_101 008 0.9052 > > 20_101 010 0.9289 > > 20_102 058 0.6924 > > 20_102 059 0.6902 > > 20_103 045 0.9778 > > 20_103 046 0.9931 > > 20_104 010 0.9324 > > 20_104 012 0.9413 > > 20_105 013 0.8754 > > 20_105 014 0.8937 > > 20_106 047 0.4433 > > 20_106 048 0.4377 > > 20_107 008 0.9178 > > 20_107 010 0.9238 > > 20_11 013 0.7631 > > 20_11 014 0.7615 > > 20_110 048 0.7687 > > 20_110 049 0.7549 > > 20_112 013 0.8821 > > 20_112 014 0.9161 > > 20_113 052 0.7689 > > 20_113 053 0.7757 > > 20_116 046 1.0072 > > 20_116 047 1.0256 > > 20_117 008 0.7742 > > 20_117 010 0.7826 > > 20_119 013 0.7929 > > 20_119 014 0.7854 > > 20_120 048 0.5090 > > 20_120 049 0.4973 > > 20_126 047 0.8285 > > 20_126 048 0.8281 > > 20_128 046 0.9580 > > 20_128 047 0.9314 > > 20_130 047 0.9439 > > 20_130 048 0.9425 > > 20_132 047 0.8550 > > 20_132 048 0.8558 > > 20_134_1 013 0.5716 > > 20_134_1 015 0.5744 > > 20_135 011 0.8357 > > 20_135 012 0.8401 > > 20_136 044 0.9995 > > 20_136 045 0.9604 > > 20_137 047 0.7922 > > 20_137 048 0.7990 > > 20_142 047 0.5282 > > 20_142 048 0.5278 > > 20_144 013 0.8755 > > 20_144 014 0.8838 > > 20_146 047 0.7997 > > 20_146 048 0.7895 > > 20_149 049 0.9251 > > 20_149 050 0.9408 > > 20_151 048 0.5905 > > 20_151 049 0.5519 > > 20_152 048 0.9024 > > 20_152 049 0.9021 > > 20_155 048 0.5285 > > 20_155 049 0.5324 > > 20_156 048 0.8883 > > 20_156 049 0.9267 > > 20_158 048 0.5404 > > 20_158 049 0.5297 > > 20_159 048 0.8021 > > 20_160 013 0.5002 > > 20_160 014 0.4942 > > 20_162 047 0.5401 > > 20_162 048 0.5401 > > 20_164 047 0.8944 > > 20_164 048 0.8940 > > 20_165 047 0.9163 > > 20_165 048 0.9077 > > 20_166 045 0.8787 > > 20_166 046 0.8848 > > 20_167 050 0.8428 > > 20_167 051 0.8442 > > 20_169 049 0.9407 > > 20_169 050 0.9462 > > 20_170 047 0.8921 > > 20_170 048 0.9113 > > 20_171 013 0.9060 > > 20_171 014 0.9060 > > 20_173 048 0.9193 > > 20_173 049 0.9141 > > 20_177 048 0.8695 > > 20_177 049 0.8600 > > 20_178 048 1.0327 > > 20_178 049 0.8979 > > 20_180 045 0.7999 > > 20_180 046 0.8002 > > 20_182 047 0.9135 > > 20_182 048 0.9130 > > 20_184 048 0.9842 > > 20_184 049 0.9960 > > 20_185 046 0.9640 > > 20_185 047 0.9514 > > 20_187 048 0.8134 > > 20_187 049 0.8082 > > 20_189 047 1.0063 > > 20_189 048 0.9701 > > 20_19 013 0.8485 > > 20_19 014 0.8534 > > 20_190 047 0.9279 > > 20_190 048 0.9169 > > 20_191 046 0.9586 > > 20_191 047 0.9751 > > 20_192 049 0.8544 > > 20_193 013 0.9084 > > 20_193 014 0.9110 > > 20_194 047 0.9220 > > 20_194 048 0.9166 > > 20_195 048 0.9552 > > 20_195 049 0.9508 > > 20_196 047 0.9098 > > 20_196 048 0.9011 > > 20_199 048 0.8569 > > 20_199 049 0.8567 > > 20_20 013 0.8750 > > 20_20 014 0.8749 > > 20_201 048 0.8864 > > 20_201 049 1.0040 > > 20_202 048 0.8542 > > 20_202 049 0.8516 > > 20_203 048 1.0267 > > 20_203 049 1.0060 > > 20_204 048 0.8513 > > 20_204 049 0.8588 > > 20_208 014 0.9130 > > 20_208 015 0.9329 > > 20_209 047 1.0020 > > 20_209 048 1.0120 > > 20_21 027 0.9747 > > 20_21 028 1.0081 > > 20_210 048 0.8607 > > 20_210 049 0.8564 > > 20_220 047 0.8888 > > 20_220 048 0.8903 > > 20_222 047 0.9998 > > 20_222 048 0.8597 > > 20_224 013 0.8122 > > 20_224 014 0.8107 > > 20_226 013 0.7855 > > 20_226 014 0.7845 > > 20_227 013 0.9372 > > 20_227 014 0.9818 > > 20_231 047 0.8355 > > 20_231 048 0.8506 > > 20_232 048 0.9730 > > 20_232 049 0.9591 > > 20_234 048 0.9357 > > 20_234 049 0.9429 > > 20_235 048 0.7528 > > 20_235 049 0.7483 > > 20_236 047 0.8997 > > 20_236 048 0.8922 > > 20_239 049 0.8920 > > 20_239 050 0.8817 > > 20_24 013 0.8197 > > 20_24 014 0.8280 > > 20_240 047 0.9109 > > 20_240 048 0.9231 > > 20_243 013 0.8227 > > 20_243 014 0.8333 > > 20_245 045 0.8620 > > 20_245 046 0.8635 > > 20_246 047 0.8236 > > 20_246 048 0.8269 > > 20_248 053 0.6015 > > 20_248 054 0.6091 > > 20_25 013 0.8676 > > 20_25 014 0.8658 > > 20_250 048 0.9124 > > 20_250 050 0.9090 > > 20_251 048 0.9061 > > 20_251 049 0.9078 > > 20_277 008 0.7923 > > 20_277 010 0.7970 > > 20_278 048 0.4834 > > 20_278 049 0.4845 > > 20_279 008 0.4363 > > 20_279 010 0.4370 > > 20_281 013 0.8672 > > 20_281 014 0.8647 > > 20_282 043 0.8884 > > 20_282 044 0.8886 > > 20_284 052 0.9152 > > 20_284 053 0.9118 > > 20_285 047 0.9546 > > 20_285 048 0.9517 > > 20_286 008 0.9607 > > 20_286 010 0.9596 > > 20_287 055 0.8976 > > 20_287 056 0.8756 > > 20_288 047 1.0127 > > 20_288 048 1.0307 > > 20_290 048 1.0089 > > 20_290 049 1.0391 > > 20_293 052 0.7792 > > 20_293 053 0.7772 > > 20_3 017 0.8530 > > 20_3 018 0.8501 > > 20_40 013 0.9392 > > 20_40 014 0.9787 > > 20_41 013 0.9562 > > 20_41 014 0.9547 > > 20_44 013 0.8725 > > 20_44 014 0.8872 > > 20_51 013 0.9420 > > 20_51 014 0.9417 > > 20_55 013 0.9796 > > 20_55 014 0.9837 > > 20_58 013 0.9677 > > 20_58 014 0.9506 > > 20_59 013 0.9180 > > 20_59 014 0.9157 > > 20_69 013 0.9265 > > 20_69 014 0.9283 > > 20_74 014 0.9476 > > 20_74 015 0.9201 > > 20_78 012 0.9822 > > 20_78 013 0.9501 > > 20_81 013 0.8664 > > 20_81 014 0.8693 > > 20_84 013 0.8827 > > 20_84 014 0.9196 > > 20_86 016 0.9138 > > 20_86 017 0.9152 > > 20_88 039 0.9905 > > 20_88 041 1.0168 > > 20_90 049 0.8263 > > 20_90 050 1.0208 > > 20_95 008 0.8892 > > 20_95 010 0.9359 > > 20_96 013 0.9191 > > 20_96 014 0.9326 > > 20_97 008 0.9569 > > 20_97 010 0.9731 > > 20_98 008 0.9317 > > 20_98 012 0.9409 > > 20_PHRU 047 0.7797 > > 20_PHRU 048 0.7894 > > > > So the registration is really poor. I've visually checked the > > registration for many of the subjects, and the functional > data isn't > > left-right reversed, I've also checked some of the > subjectname files > > (which I created by running a script) and they are correct. > > > > I'm new to Freesurfer, so maybe I've made a mistake > somewhere? I'm > > been following these instructions: > > > > https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastTutorial > > > > Thanks, > > Keri > > > > > > On Fri, Jan 18, 2019 at 6:44 PM Greve, Douglas N.,Ph.D. > > <DGREVE(a)mgh.harvard.edu<mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu<mailto:DGREVE@mgh.harvard.edu>> > <mailto:DGREVE@mgh.harvard.edu<mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu<mailto:DGREVE@mgh.harvard.edu>>>> wrote: > > > > What version of FS are you using? version 6 initializes with > > mri_coreg (the FS equivalent of spm_coreg). On > whole-brain data, > > I've found this to be very robust. Is your data whole-brain? > > > > On 1/18/19 5:10 AM, Keri Woods wrote: > >> > >> External Email - Use Caution > >> > >> Hi > >> > >> I have a problem very similar to this one: > >> > >> > https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg23206.html > >> > >> I've tried the suggestions given there, but it didn't > fix my problem. > >> > >> I'm running the FSFAST preproc-sess stream and the > quality of the > >> registration is very poor for most of the subjects. > >> > >> I've tried initializing the registration differently, using > >> bbregister with --init-fsl, --init-spm and init-header, > which > >> didn't improve the results at all. > >> > >> I've also tried register-sess with --init-fsl, > --init-spm and > >> init-header, as well as spmregister-sess and > fslregister-sess. > >> > >> Is there anything else I could try? > >> > >> Using the SPM GUI, the registration was fine, so I > thought that > >> spmregister-sess would have been an improvement, but it > wasn't. > >> Is there anyway I can import the registration obtained > using the > >> SPM GUI? > >> > >> Thanks for your help. > >> > >> Thanks, > >> Keri > >> > >> > >> > >> > >> > >> _______________________________________________ > >> Freesurfer mailing list > >> Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>> > <mailto:Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>>> > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>> > <mailto:Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Mismatch between ?h.BA.thresh.annot and ?h.entorhinal.thresh.label/?h.perirhinal.thresh.label
by Yi Leng Fung 02 Feb '19

02 Feb '19

External Email - Use Caution Dear FreeSurfer Developers, I ran -recon-all -all on my subjects with the aim of examining the gray volumes of the ex vivo entorhinal and perirhinal cortex. Prior to extracting the gray volume numbers of the entorhinal and perirhinal cortex from ?h.BA_exvivo.thresh.stats file, I was examining the entorhinal and perirhinal cortex on the ?h.BA.thresh.annot on Freeview. However, I noted that their locations on the annot file did not correspond to the locations indicated by ?h.entorhinal.thresh.label and ?h.perirhinal.thresh.label. I have also loaded the annot files and label files from the fully recon-ed subject named "bert" on Freeview and observed the same mismatch in the labeling. I am curious why this might be the case. For your reference, I have uploaded a few screenshots from Freeview, on "bert", to demonstrate the label names in the annot file, both with and without the outline of the label files. I have searched the archive and have not been able to find any similar queries on this, hence it would be of tremendous help if someone could clarify this observation. If it is of interest, I am running freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0 on Ubuntu 16.04. Thank you for your assistance and I look forward to hearing from you. Best regards, *Yi-Leng*

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Re: [Freesurfer] Trouble Installing FreeSurfer {Disarmed}
by fsbuild 01 Feb '19

01 Feb '19

External Email - Use Caution Hello Rodrigo, Please use capital -C and not lowercase -c to tell the tar command what directory to untar the files into; you used -C the first time when the file could not be found, but on the subsequent commands you changed it to -c  - R. tar -C /eeg/local -xzvf freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0.tar..gz Rodrigo Montenegro at 13:42 2/01/2019         External Email - Use Caution        Hey! I have not received any feedback from that… Not sure if the mail was lost?...  Any help would be appreciated! Kind Regards, Rodrigo Montenegro+44(0)7503070807 From: Rodrigo Montenegro [mailto:rmontenegro11@gmail.com] Sent: 30 January 2019 20:39 To: 'Freesurfer support list' <freesurfer(a)nmr.mgh.harvard.edu> Cc: 'rodrigo.montenegro(a)ndcn.ox.ac.uk' <rodrigo.montenegro(a)ndcn.ox.ac.uk> Subject: RE: [Freesurfer] Trouble Installing FreeSurfer {Disarmed} Importance: High Hi R, Thanks for the quick response. I have but still couldn’t go through the process. I have also read your e-mail but I have no idea what you refer to in your second e-mail. This is what I have got:  Kind Regards, Rodrigo Montenegro+44(0)7503070807 From: freesurfer-bounces(a)nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of fsbuild Sent: 28 January 2019 23:17 To: freesurfer(a)nmr.mgh.harvard.edu Cc: rodrigo.montenegro(a)ndcn.ox.ac.uk Subject: Re: [Freesurfer] Trouble Installing FreeSurfer {Disarmed}         External Email - Use Caution        … Correction - with the v switch “tar -xzvf” it is going to list every fileit expands and then return to the “$” prompt. - R._______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Postdoctoral position in Eating Disorders at UCSD
by Grethe, Amanda 01 Feb '19

01 Feb '19

External Email - Use Caution Research Postdoctoral Fellowship at UC San Diego’s Eating Disorders Center for Treatment and Research The University of California, San Diego Eating Disorders Center for Treatment and Research is an international leader in research on the neurobiology of eating disorders and related problems. We have IOP and day treatment programs for adults, adolescents, and children with eating disorders, as well as a medical stabilization unit in conjunction with Rady Children’s Hospital. UCSD EDC’s programs are growing quickly, and we are currently accepting applications for postdoctoral fellows. Current eating disorder treatments are of limited efficacy. New insight into neurobiological mechanisms that contribute to symptoms is supporting development of more effective interventions. The UCSD program is unique in that it has faculty and staff who focus on combining research into neurobiology with treatment development. This is an exciting opportunity for individuals to learn about brain and behavior and apply this knowledge to new treatment approaches. We also encourage applications from candidates who come from backgrounds outside of eating disorders, particularly anxiety, substance use, trauma, or pediatrics, and we have a strong preference for candidates who have experience or interest in functional neuroimaging. Many of our postdocs stay on in permanent staff or faculty positions. Research Postdoctoral Position Research postdoctoral fellow: to specialize in studying mechanisms underlying eating disorder symptoms and psychopathology (e.g., incentive processing, reinforcement learning, interoception). Experience and interest in neuroimaging (functional MRI, structural MRI) and neurocognitive assessment is preferred, as we have a strong neuroimaging program conducting research on the neurobiology of ED. The position will entail immersion in MR image analysis using one or more software tools, including AFNI, FSL, SPM, FreeSurfer, and R. Imaging sessions will take place at UCSD’s Center for Functional MRI, which is equipped with two research-dedicated GE 3T short-bore scanners. Experience with other experimental methodologies is also welcome. The ideal candidate would be a research-oriented person with a goal of an independent research career focused on cognition, brain functioning, and treatment development to translate research findings to improved clinical care of individuals with an eating disorder. Many of our research postdocs write training grants and transition to permanent staff or faculty positions. Appointment length is up to 2 years and is based upon the UC post-doctoral scholar salary scale. The position is available the summer of 2019, and applications will be accepted until the position is filled. Required qualifications • PhD in Clinical Psychology or related area • Experience in neurocognitive assessment preferred • Experience in neuroimaging or similar methods preferred • Preference for strong background and training in cognitive neuroscience and statistics • Established track record of publications To apply for this position, please email a cover letter, CV, and three references to Christina Wierenga, PhD (cwierenga(a)ucsd.edu<mailto:cwierenga@ucsd.edu>) and Amanda Bischoff-Grethe, PhD (agrethe(a)ucsd.edu<mailto:agrethe@ucsd.edu>). ---- Amanda Bischoff-Grethe Associate Adjunct Professor University of California, San Diego 9500 Gilman Drive MC 0738 La Jolla, CA 92093-0738 Tel: 858-246-0604 Fax: 858-246-0556

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Re: [Freesurfer] Trouble Installing FreeSurfer {Disarmed}
by fsbuild 01 Feb '19

01 Feb '19

External Email - Use Caution … Correction - with the v switch “tar -xzvf” it is going to list every fileit expands and then return to the “$” prompt. - R. On , at 18:11  1/28/2019, fsbuild <fsbuild(a)contbay.com> wrote:        External Email - Use Caution        Hello Rodrigo,Did you download the tar file freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0.tar.gz from this page, and attempt to follow the steps below ?https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstallIf you do not have permission to untar (write files) into /usr/local, you could try using another path. But usually if the tar command has a problem it will echo some error/text to the terminal, e.g., "Permission denied", or say there was an error.If the command simply returns to the prompt than it should have succeeded, e.g., success with "$" bash shell prompt.$ tar -C /usr/local -xzvf freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0.tar.gz$Please try and point out the step that does not work for you.- R.On , at 17:47  1/28/2019, Rodrigo Montenegro <rmontenegro11(a)gmail.com> wrote:        External Email - Use Caution        Dear FreeSurfer Team, I’m a Medicine student at Oxford University and I have just registered to FreeSurfer. I just went through the registration process so I'm very new to FreeSurfer but have only run to problems so far and would like to ask for your help: 1.       I have register with FreeSurferWiki but can’t login: it gives me one of the following errors:i.                      “Error 403 Login/Edit allowed only on https/SSL connections Login/Edit allowed only on https/SSL connections Guru Meditation: XID: 1153030795 Varnish cache serve”.ii.                   Or that it is an “Invalid username or password” (not sure if  2.       More importantly I have also tried to install FreeSurfer in Virtual Box (4096 MB Memory; 32 MD Video Memory; Ubuntu 64 Bits) without any success. The Ubuntu system works fine and I have the “freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0.tar.gz” to install FreeSurfer but the being totally new to Linux I have not had success to install it:i.                     I’m not sure if at all the files are unzipped from the .gz file.ii.                   And I have been unable to create the Bash files to define the environment for it. 3.        Finally, I notice that you do have an installation for Virtual Disk Image but the download for it (ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0/freesurfer-Virtu…) is a gz file not a .vdi file as it should be (see picture below): <image002.jpg> So either way I wasn’t able to get through with the installation and any help is appreciated. Could you please provide some advice? Many thanks, Rodrigo Montenegro+44(0)7503070807 _______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

3 3

Freesurfer Recon-all error
by Jones, Kevin 01 Feb '19

01 Feb '19

3 5

Pb testing the FreeSurfer Installation
by Lise_A 01 Feb '19

01 Feb '19

External Email - Use Caution Dear Sir or Madam, I've just installed the last version of FreeSurfer for Linux ( freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0.tar.gz <https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0/freesurfer-Lin…>), but I got some troubles testing it: When trying to follow Example 2 ( https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall#Download) I get a "syntax error message": lise.aujoulat@ICM-COHEN-LF001 ~ $ *export SUBJECTS_DIR=/home/lise.aujoulat/Bureau/SUBJECTS_DATA* lise.aujoulat@ICM-COHEN-LF001 ~ $ * bash recon-all -i sample-001.nii.gz -s bert -all/usr/local/freesurfer/bin/recon-all: recon-all: ligne 31: erreur de syntaxe près du symbole inattendu « ( »/usr/local/freesurfer/bin/recon-all: recon-all: ligne 31: `set inputargs = ($argv);'* You can find a screen shot attached to this email. It seems that no one encountered this problem so far. I had installed the macOS version some months ago on my personal computer and encountered no problem at that time. How could I fix this? Thanks for your help, Lise -- Lise AUJOULAT MSc student in Integrative Biology and Physiology, Sorbonne University, Paris, France. Phone number: + 33 6 87 97 30 32 Mail: aujoulat.lise(a)gmail.com / lise.aujoulat(a)etu.upmc.fr

3 4

Error with trac-all -path
by Seider, Nicole 31 Jan '19

31 Jan '19

External Email - Use Caution Dear all, I am having an error with the final step of TRACULA, trac-all -path. For a single subject (of a set of 38), when processing pathway 2 of 18, I will get the following error message: Segmentation fault (core dumped). For all other subjects, all the pathways are tracked successfully. I have double checked that all the paths are correct, that all the necessary files from previous steps exist (as suggested on other error mailing lists). Looking through the error file, I can't find anything in particular that seems to have failed. Any suggestions? Three files are attached: trac-all.error, trac-all.log, and trac-all_cluster-bedp.log. We ran the second step (trac-all -bedp) on our cluster, so it's log file is seperate. Thank you, Nicole Seider Neuroscience Graduate Student Washington University in St Louis nicole.seider(a)wustl.edu

1 0

problems with Freeview
by Laboratorio de Neurociencia Funcional 31 Jan '19

31 Jan '19

External Email - Use Caution Dear Freesurfers, we have installed the updated Freeview version in the development version of Freesurfer (Centos 6, 18 january build), but Bert images appear displaced when they are loaded with this version of Freeview. The same displacement occurs when other dataset is used. Please find attached a screenshot to display the issue. Would you please help me to solve the problem? Thank you in advance. Best, Jose

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