External Email - Use Caution Hi Douglas,
Thanks a lot for your kind explanation! With regards Vittal On Thu, Dec 17, 2020 at 8:12 PM <freesurfer-requ...@nmr.mgh.harvard.edu> wrote: > Send Freesurfer mailing list submissions to > freesurfer@nmr.mgh.harvard.edu > > To subscribe or unsubscribe via the World Wide Web, visit > > https://secure-web.cisco.com/1d5gSB-rqVInM6onHMLDbLhUREGgzCvmI5zHvbuwq-S_PJCuw3EMc2kV4eq7chGX405ndWxjVJST5a2MbctIecDLR4jHj04tzIjlJ-K7sRsBSXoEHazGQR-uVM6rudDyR3Y7AQdBZKN8dtBn7OKIjFZVtUqZrOpgRSs_YB6U1oRHHI1srOBKZMXCRbkMkqN4s6POAVqoNSpgM_OA-E6E20iqNg7LlTqjMfc_o7LATYKEK3dYGTrk8OoLqWVwO9U3mBsRw9E6-T1zhH7qaRm4vJA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer > or, via email, send a message with subject or body 'help' to > freesurfer-requ...@nmr.mgh.harvard.edu > > You can reach the person managing the list at > freesurfer-ow...@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: HCP_1200 parcellation problems (Greve, Douglas N.,Ph.D.) > 2. Re: need assistance to decode QDEC results > (Greve, Douglas N.,Ph.D.) > 3. Re: Cortical thickness volume ROI to surface {Disarmed} > (Greve, Douglas N.,Ph.D.) > 4. Re: Error in selxavg3-sess (Greve, Douglas N.,Ph.D.) > 5. Re: cannot find freesurfer/average/RB_all_2008-03-26.gca with > -use-gpu in v5.3 (Greve, Douglas N.,Ph.D.) > 6. Re: cannot find freesurfer/average/RB_all_2008-03-26.gca with > -use-gpu in v5.3 {Disarmed} (Caspar M. Schwiedrzik) > 7. Re: group analyses {Disarmed} (Greve, Douglas N.,Ph.D.) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 17 Dec 2020 14:28:37 +0000 > From: "Greve, Douglas N.,Ph.D." <dgr...@mgh.harvard.edu> > Subject: Re: [Freesurfer] HCP_1200 parcellation problems > To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu> > Message-ID: <786b64c3-2d99-06ed-2fe3-812225238...@mgh.harvard.edu> > Content-Type: text/plain; charset="utf-8" > > Sorry, I can't tell from your email what the problem is. Can you elaborate? > > On 12/9/2020 2:30 PM, najme soleimani wrote: > > External Email - Use Caution > > Dear FreeSurfer Developers, > I downloaded the HCP_1200 subjects' structural extended data. I am > attempting to have equal sized parcellation on scale 100, so I used > parcellation results of Desikan atlas and increased the parcels from 68 to > 100. > after obtaining split file, I run the following commands on FreeSurfer: > mris_divide_parcellation subj lh aparc.annot splitfile Desikan100 > mris_divide_parcellation subj rh aparc.annot splitfile Desikan100 > mri_aparc2aseg --s subj --annot Desikan100 --old-ribbon --o > $SUBJECTS_DIR/subj/mri/Desikan100.subj.mgz > The interesting part is that after running this command some > disconnectivity were seen in the parcels as it is shown in the picture. In > 3D view, also, when the parcels were loaded on dsi studio, there were some > holes on the parcels which caused disconnected parcels. > I will appreciate if you help me to solve this problem. > > > kind regards, > Najme > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> > https://secure-web.cisco.com/1d5gSB-rqVInM6onHMLDbLhUREGgzCvmI5zHvbuwq-S_PJCuw3EMc2kV4eq7chGX405ndWxjVJST5a2MbctIecDLR4jHj04tzIjlJ-K7sRsBSXoEHazGQR-uVM6rudDyR3Y7AQdBZKN8dtBn7OKIjFZVtUqZrOpgRSs_YB6U1oRHHI1srOBKZMXCRbkMkqN4s6POAVqoNSpgM_OA-E6E20iqNg7LlTqjMfc_o7LATYKEK3dYGTrk8OoLqWVwO9U3mBsRw9E6-T1zhH7qaRm4vJA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://secure-web.cisco.com/1N-WHwF2EBhYVgmPPGae-ZczRxVkwJb1tLaQmhwnqe1R8ElMo8vU-u8oQjxinF0OsxMPgxjxP1NkTeVH7VpsuyXqz_0CmWth3PRarrPET8mS8nXplM5fw4u6XjeL2PuR-WEJ9OhJnhJ0JnXu_VeHPRPPNBDddTF0xL2NH3OkAh6fJvu2VKNklo34sPuribZdUIOLvAHwY5r1IpBmHv6K8bcNNmqhsIG0xsBTwwYQhYtBKFTxgKgebPibgj-BnyDVFM1__1122U-1geEPzfGOMCw/http%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fpipermail%2Ffreesurfer%2Fattachments%2F20201217%2Fe3effd94%2Fattachment-0001.html > > ------------------------------ > > Message: 2 > Date: Thu, 17 Dec 2020 14:27:36 +0000 > From: "Greve, Douglas N.,Ph.D." <dgr...@mgh.harvard.edu> > Subject: Re: [Freesurfer] need assistance to decode QDEC results > To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu> > Message-ID: <e914c43c-e317-147d-41cc-faf9b0133...@mgh.harvard.edu> > Content-Type: text/plain; charset="utf-8" > > It depends on the order that you specified them. You will have four groups > SczUrban > SczRural > HVUrban > HVRural > > The interaction will be of the form > (SczUrban-SczRural)-(HVUrban-HVRural) > > Look in the y.fsgd to see what the order of the classes is. You can then > look in the contrast folder at C.dat to get the + and - 1s used in the > contrast. > > On 12/9/2020 12:58 PM, vittal korann wrote: > > External Email - Use Caution > > Dear FreeSurfer experts, > > I was running group interaction (for diagnosis and birthplace) in QDEC > with gyrification as a dependent variable and age, gender as nuisance > factors. > In diagnosis, we have 2 groups: i) schizophrenic patients ii) healthy > volunteers. > Similarly, birthplace has 2 groups: i) urban ii) rural birth > > For the above-said design, I got reddish yellow color results in the > display tab of Qdec. > So, my query is that do results indicate that patients who were born in > urban have a higher gyrification index than healthy volunteers who born in > urban or something else? Do I sound correct in decoding the interaction > results? If not please let me know the exact meaning of the results. > > Looking forward to hearing from you. > > Thanks, > Vittal > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> > https://secure-web.cisco.com/1d5gSB-rqVInM6onHMLDbLhUREGgzCvmI5zHvbuwq-S_PJCuw3EMc2kV4eq7chGX405ndWxjVJST5a2MbctIecDLR4jHj04tzIjlJ-K7sRsBSXoEHazGQR-uVM6rudDyR3Y7AQdBZKN8dtBn7OKIjFZVtUqZrOpgRSs_YB6U1oRHHI1srOBKZMXCRbkMkqN4s6POAVqoNSpgM_OA-E6E20iqNg7LlTqjMfc_o7LATYKEK3dYGTrk8OoLqWVwO9U3mBsRw9E6-T1zhH7qaRm4vJA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://secure-web.cisco.com/14fogu9zmLf4Ph1wPxk5IYAaluFaGJIKAAfLcrnE7dBmNLeHKloLbH0R7GG5t2ck1QYDSjlsqbfZsTFOH22yKfCpKvaWcpYfoQtMwFQl8eGOI8lKQ7hzteAVPP_xpTPlkEVYzA9OsFIhJDTuoMsusIr0NPa8Q8pAEYPQ-AQHBZVMxbNJRJGktGlA-clo-27AmGFQtU0oxqc6m15iYBDI3j8LthZDuJ_qAJ20H57h86H4gZ1DZX8gjNk4mgJeye23T3ZKmtTkGalo-bMbhewiVgA/http%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fpipermail%2Ffreesurfer%2Fattachments%2F20201217%2F3970303d%2Fattachment-0001.html > > ------------------------------ > > Message: 3 > Date: Thu, 17 Dec 2020 14:31:03 +0000 > From: "Greve, Douglas N.,Ph.D." <dgr...@mgh.harvard.edu> > Subject: Re: [Freesurfer] Cortical thickness volume ROI to surface > {Disarmed} > To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu> > Message-ID: <0b70fc8e-b0ef-b16c-ba84-c1f6aaabb...@mgh.harvard.edu> > Content-Type: text/plain; charset="utf-8" > > fslregister should have printed out a tkregisterfv command to use to check > the registration. Does that registartion look ok or not? If not, try > mri_coreg instead of fslregister > > On 12/11/2020 6:11 AM, Alina Rojas wrote: > > External Email - Use Caution > > Hello Douglas, > > Thank you for your response. I seem to be having problems with > registration. I tried: > > #flirt -in T1w.nii.gz -ref fsl/data/standard/MNI152_T1_2mm -out > T1w_MNI.nii.gz -omat T1w_MNI.mat#fnirt --in=T1w.nii.gz --aff=T1w_MNI.mat > --cout=nonlinear_transf --config=T1_2_MNI152_2mm#applywarp > --ref=/fsl/data/standard/MNI152_T1_2mm --in=T1w.nii.gz > --warp=nonlinear_transf --out=warped_strucctural > > ->>this looks good, the ROI is where I expect it to be. > > [cid:part1.A0715EA3.F1997B19@mgh.harvard.edu][ > cid:part2.832C2D59.D5A0FCB1@mgh.harvard.edu] > > > #fslregister --s fsaverage --mov T1w_MNI.nii.gz --reg > /work/bav5809/subjects/severe/freesurfer_output/hand/${SUBJECTID}-${SESSIONID}/tmp.dat > > #tkmeditfv fsaverage T1.mgz \ > -overlay M1_L_bin.nii.gz \ > -overlay-reg tmp.dat \ > -fthresh 0.5 \ > > ->>the problems seems to be in the registration because that does not look > good. > [cid:part3.9F6D9A90.70B6235B@mgh.harvard.edu] > > Can you help me find the problem? > > Many thanks, > > Alina Rojas > > Am 29.11.2020 um 18:17 schrieb Greve, Douglas N.,Ph.D. < > dgr...@mgh.harvard.edu<mailto:dgr...@mgh.harvard.edu>>: > > Have you checked that the output of each of the stages is correct? Eg, > does mydata_T1.nii.mgz overlay with MNI152 and with ROI_MNI? At the end of > fslregister, there will be a tkregister command to visualize the > regsitration. Do those look ok? > > On 11/17/2020 4:48 AM, Alina Rojas wrote: > > External Email - Use Caution > > Thank you for your response! Here the commands: > > > #register image to MNIspace > flirt -in mydata_T1.nii.gz -ref fsl/data/standard/MNI152_T1_1mm -out > mydata_T1_MNI.nii.gz -omat mydata_T1_MNI.mat > #Create a registration from the ROI-anatomical volume to a freesurfer > template subject > fslregister --s fsaverage --mov mydata_T1_MNI.nii.gz --reg tmp.dat > #Map the ROI-mask to the fsaverage surface, to create an fsaverage-ROI > surface overlay. > mri_vol2surf --mov ROI_MNI.nii.gz --reg tmp.dat --projdist-max 0 1 0.1 > --interp nearest --hemi lh --out lh.fsaverage.ROI_MNI.mgh ?noreshape > tkmeditfv fsaverage lh inflated -overlay lh.fsaverage.M1_L.mgh -fthresh 0.5 > > I tried with another threshold, and to change it while in Freeview and > it?s either the whole surface with the overlay or none. > > Thank you for your help! > > Alina Rojas > > > > > Am 16.11.2020 um 17:04 schrieb Douglas N. Greve <dgr...@mgh.harvard.edu > <mailto:dgr...@mgh.harvard.edu>>: > > please send the command line > > On 11/16/2020 7:20 AM, Alina Rojas wrote: > > External Email - Use Caution > > Hello Freesurfer experts, > > I am attempting to register a ROI (.nii) to the surface of fsaverage to > get the statistical output on the cortical thickness. I followed your > instructions on MailScanner has detected a possible fraud attempt from " > secure-web.cisco.com" claiming to behttps:// > surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness< > https://secure-web.cisco.com/1vMR3HBqveQVdV1izVoGaJ5VcRtbR7HBn6ADoe1ai7ok5utz9wmCB_PLEjDtsOmyziziVBQRSmBgczrdyk56eX0vaBWBNP1iIevBdxOho3o-JJ64DuVK1J6XpzIFNVqqzBDHDrU6O2cYjWTNnglb4Ow4OIdXr5Qq28eboicyUSvLl2KmB0P0lQY9abQIfjX6hs_1Q1FvwX1Tx7YnGwsbJIgqcpDRG0dkvqZc0pgeiBQbnNjLadwozbHME2Ale8Kt0-V-I2Urmgq5zbEhzlAPvCA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FVolumeRoiCorticalThickness> > but after mri_vol2surf I get this message, I can?t visualize the ROI on the > surface. I I?m using Freesurfer 7.0.1. How can I solve this? Thank you, > Alina Rojas. > > srcvol = M1_L.nii.gz > srcreg = tmp.dat > srcregold = 0 > srcwarp unspecified > surf = white > hemi = lh > ProjDist = 0.5 > reshape = 0 > interp = nearest > float2int = round > GetProjMax = 1 > INFO: float2int code = 0 > INFO: using NIfTI-1 qform > Done loading volume > INFO: This REGISTER_DAT transform is valid only for volumes between COR > types with c_(r,a,s) = 0. > Input reg is register.dat > -------- original matrix ----------- > 1.00000 0.00000 0.00000 2.49380; > 0.00000 0.00000 1.00000 -22.50500; > 0.00000 -1.00000 0.00000 -9.53872; > 0.00000 0.00000 0.00000 1.00000; > -------- original matrix ----------- > Reading surface /fsaverage/surf/lh.white > Done reading source surface > Mapping Source Volume onto Source Subject Surface > 1 0 0 1 > using old > 2 0.1 0 1 > using old > 3 0.2 0 1 > using old > 4 0.3 0 1 > using old > 5 0.4 0 1 > using old > 6 0.5 0 1 > using old > 7 0.6 0 1 > using old > 8 0.7 0 1 > using old > 9 0.8 0 1 > using old > 10 0.9 0 1 > using old > Done mapping volume to surface > Number of source voxels hit = 75073 > Writing to lh.fsaverage.M1_L.mgh > Dim: 163842 1 1 > surfcolor: Subscript out of range. > > > > > > > _______________________________________________ > Freesurfer mailing list > 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 > https://secure-web.cisco.com/1d5gSB-rqVInM6onHMLDbLhUREGgzCvmI5zHvbuwq-S_PJCuw3EMc2kV4eq7chGX405ndWxjVJST5a2MbctIecDLR4jHj04tzIjlJ-K7sRsBSXoEHazGQR-uVM6rudDyR3Y7AQdBZKN8dtBn7OKIjFZVtUqZrOpgRSs_YB6U1oRHHI1srOBKZMXCRbkMkqN4s6POAVqoNSpgM_OA-E6E20iqNg7LlTqjMfc_o7LATYKEK3dYGTrk8OoLqWVwO9U3mBsRw9E6-T1zhH7qaRm4vJA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer< > 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http://secure-web.cisco.com/1RVCqpuZsIK9379y92Kn__aB-V_OsvWUCZiqktENPiR-S1bEv7BfssaXYrzOViGAFM030hPV7KqE6mDZ7DcqkXswbkZEucU0FmEjPgyo0A-qYA80KqcpEpXhcMVX_mIAQZopwOMqowb_1vDa7EpE0y94r0mYwwYNWoAhskAURQzUQsxLHCyjMNo-og2MZeinTmgp-CvzFGPDbTt3Xg8Rnnr-Ld3EyifpPKoDtw6Gvxhbsc0A3a8oKSGeqVM-Mj1NsePlRNTHJsdPFm9-QI_0PYQ/http%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fpipermail%2Ffreesurfer%2Fattachments%2F20201217%2F57b27913%2Fattachment-0005.png > > ------------------------------ > > Message: 4 > Date: Thu, 17 Dec 2020 14:34:29 +0000 > From: "Greve, Douglas N.,Ph.D." <dgr...@mgh.harvard.edu> > Subject: Re: [Freesurfer] Error in selxavg3-sess > To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu> > Message-ID: <7226e63d-3bff-bbd2-a211-6d9561a6b...@mgh.harvard.edu> > Content-Type: text/plain; charset="utf-8" > > Are there presentations that are simultaneous? > > On 12/12/2020 3:19 AM, Nina Khatibi wrote: > > External Email - Use Caution > > Hi, > I'm using a functional analyse with selxavg3-sess, i have 25 subjects and > each subject contains 15 runs, I've done plenty of analyses with different > paradigm files, but now with a paradigm file of 5 conditions, I face an > error on subject 22 run 12, which I can not solve.I wonder if you can help > me. > I'm using macbook pro 2018, macOS Mojave 10.14.6 and > freesurfer-darwin-macOS-7.1.1-20200811-8b40551 > > > outanadir = > /Volumes/ADATA/FunctionalData/Subject22/bold/fsaverage5Con2Sec.lh/pr012 > > Excluding 4 points > > ERROR: fast_st2fir: two or more presentations are simultaneous > > ERROR: creating FIR design matrix for Condition01 > > Dot indexing is not supported for variables of this type. > > > Error in flac_customize (line 354) > > if(~isempty(flacnew.TFmtx)) > > > Error in fast_selxavg3b (line 179) > > flac = flac_customize(flac); > > > > >> ------------------------------------------ > > ERROR: fast_selxavg3() failed\n > > > Regards, > > Nina > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> > https://secure-web.cisco.com/1d5gSB-rqVInM6onHMLDbLhUREGgzCvmI5zHvbuwq-S_PJCuw3EMc2kV4eq7chGX405ndWxjVJST5a2MbctIecDLR4jHj04tzIjlJ-K7sRsBSXoEHazGQR-uVM6rudDyR3Y7AQdBZKN8dtBn7OKIjFZVtUqZrOpgRSs_YB6U1oRHHI1srOBKZMXCRbkMkqN4s6POAVqoNSpgM_OA-E6E20iqNg7LlTqjMfc_o7LATYKEK3dYGTrk8OoLqWVwO9U3mBsRw9E6-T1zhH7qaRm4vJA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://secure-web.cisco.com/192yRSHaanmI9rKiKSMibkT-Msp3Qml-y-_YsDeztlrvSWyPYcbHSWhXC6YVcKLySegQm4-w7N-pMXImQyXB2r_o05fvtwYmXnga1EW-sqMSrRWREBXrIRBdJeXhe8NaHSrItQjqrtVzOp5u5p9vZ-AFBN8jgE920NGtgJbUQKxBevDfIYiEFOjAP1ya6NmwkZySzVzsoDFJuP1HmXCnyB2EZ0ZhLv-l-8uxSjXhMhYkXUpbvEbRwGHQLcmfePB3cMY-se-ycUdNsCf6FplPXZg/http%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fpipermail%2Ffreesurfer%2Fattachments%2F20201217%2F4d4f28b7%2Fattachment-0001.html > > ------------------------------ > > Message: 5 > Date: Thu, 17 Dec 2020 14:36:39 +0000 > From: "Greve, Douglas N.,Ph.D." <dgr...@mgh.harvard.edu> > Subject: Re: [Freesurfer] cannot find > freesurfer/average/RB_all_2008-03-26.gca with -use-gpu in v5.3 > To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu> > Message-ID: <fb0d461f-dc8c-9ce7-e906-8917950e2...@mgh.harvard.edu> > Content-Type: text/plain; charset="utf-8" > > The GPU stuff may or may not work. It was hard to maintain because the > GPUs kept changing so much, and it would not surprise me that the code from > 5.3 is incompatable with GPUs today. But it looks like the error is that it > could not find a file. Does that file actually exist? > > On 12/12/2020 3:04 PM, Caspar M. Schwiedrzik wrote: > > External Email - Use Caution > > Hi! > I am trying to run recon-all in version 5.3 with the -use-gpu flag. I am > getting a strange error that I would love to get your input on: cannot > find freesurfer/average/RB_all_2008-03-26.gca > Neither the file nor the path exist. > > This is the entire input and output: > > recon-all -s hum_14600_parallel -i > /neuro_tools/freesurfer/subjects/hum_14600/mri/011/mp2rage.nii -all -use-gpu > Testing for CUDA device: > nvcc: NVIDIA (R) Cuda compiler driver > Copyright (c) 2005-2012 NVIDIA Corporation > Built on Fri_Sep_21_17:28:58_PDT_2012 > Cuda compilation tools, release 5.0, V0.2.1221 > > Driver : 10.0 > Runtime : 5.0 > > Acquiring CUDA device > Using default device > CUDA device: Tesla K40m > > > ======= NUMBER OF OPENMP THREADS = 1 ======= > stable5 > > NVIDIA driver version info: > NVRM version: NVIDIA UNIX x86_64 Kernel Module 410.79 Thu Nov 15 > 10:41:04 CST 2018 > > ERROR: cannot find /neuro_tools/freesurfer/average/RB_all_2008-03-26.gca > > Is there some documentation on how to set up the environment beyond > LD_LIBRARY_PATH? Could that be the issue? Everything works fine without the > -use-gpu flag. > > Thank you! Caspar > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> > https://secure-web.cisco.com/1d5gSB-rqVInM6onHMLDbLhUREGgzCvmI5zHvbuwq-S_PJCuw3EMc2kV4eq7chGX405ndWxjVJST5a2MbctIecDLR4jHj04tzIjlJ-K7sRsBSXoEHazGQR-uVM6rudDyR3Y7AQdBZKN8dtBn7OKIjFZVtUqZrOpgRSs_YB6U1oRHHI1srOBKZMXCRbkMkqN4s6POAVqoNSpgM_OA-E6E20iqNg7LlTqjMfc_o7LATYKEK3dYGTrk8OoLqWVwO9U3mBsRw9E6-T1zhH7qaRm4vJA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://secure-web.cisco.com/1g9GPCczmd0TeozQaEnXqD5nmo0hYTbVdBE7zUUpB5fg1i6CB4R2dncT7ZBIz7NlB-5sC-tZh9ZQ79asQxVF765WPfeCBMOoa1HLYtS26NkUdTybj7UZJEpcfWhK-J30FHZf6cRs0Ei5ZQnp9LbNON5KdFaa4lOJlWgxlrgjzBdvv5YNZI0vGLy7sDU9eeI1NQf8tCG3VTjSk717DihiD7DuCwrM6l_hM2fMx0gVmWwmXgcVu_iSLcuBTS4-gf7slxnMKtvb0-OQvt661IoBbcA/http%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fpipermail%2Ffreesurfer%2Fattachments%2F20201217%2F9828b098%2Fattachment-0001.html > > ------------------------------ > > Message: 6 > Date: Thu, 17 Dec 2020 15:38:46 +0100 > From: "Caspar M. Schwiedrzik" <cschwie...@rockefeller.edu> > Subject: Re: [Freesurfer] cannot find > freesurfer/average/RB_all_2008-03-26.gca with -use-gpu in v5.3 > {Disarmed} > To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > Message-ID: > < > ca+bx-39lxrwm97vponuybd+l-juakunvm8voqfvqxrxlsi8...@mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > External Email - Use Caution > > Hi Doug, > it turns out part of the v5.3 installation had been accidentally deleted. > After restoring the file, it works fine, and I am happy to report the the > GPU versions work (with CUDA 5). > Thanks! > Caspar > > > Am Do., 17. Dez. 2020 um 15:37 Uhr schrieb Greve, Douglas N.,Ph.D. < > dgr...@mgh.harvard.edu>: > > > The GPU stuff may or may not work. It was hard to maintain because the > > GPUs kept changing so much, and it would not surprise me that the code > from > > 5.3 is incompatable with GPUs today. But it looks like the error is that > it > > could not find a file. Does that file actually exist? > > > > On 12/12/2020 3:04 PM, Caspar M. Schwiedrzik wrote: > > > > External Email - Use Caution > > Hi! > > I am trying to run recon-all in version 5.3 with the -use-gpu flag. I am > > getting a strange error that I would love to get your input on: cannot > > find freesurfer/average/RB_all_2008-03-26.gca > > Neither the file nor the path exist. > > > > This is the entire input and output: > > > > recon-all -s hum_14600_parallel -i > > /neuro_tools/freesurfer/subjects/hum_14600/mri/011/mp2rage.nii -all > -use-gpu > > Testing for CUDA device: > > nvcc: NVIDIA (R) Cuda compiler driver > > Copyright (c) 2005-2012 NVIDIA Corporation > > Built on Fri_Sep_21_17:28:58_PDT_2012 > > Cuda compilation tools, release 5.0, V0.2.1221 > > > > Driver : 10.0 > > Runtime : 5.0 > > > > Acquiring CUDA device > > Using default device > > CUDA device: Tesla K40m > > > > > > ======= NUMBER OF OPENMP THREADS = 1 ======= > > stable5 > > > > NVIDIA driver version info: > > NVRM version: NVIDIA UNIX x86_64 Kernel Module 410.79 Thu Nov 15 > > 10:41:04 CST 2018 > > > > ERROR: cannot find /neuro_tools/freesurfer/average/RB_all_2008-03-26.gca > > > > Is there some documentation on how to set up the environment beyond > > LD_LIBRARY_PATH? Could that be the issue? Everything works fine without > the > > -use-gpu flag. > > > > Thank you! Caspar > > > > > > _______________________________________________ > > Freesurfer mailing listfreesur...@nmr.mgh.harvard.eduhttps:// > mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer < > https://secure-web.cisco.com/1u8Ty-7RI3vSX7RlSR_BpQW5VC3KUVp2GWUyiLCQ7zycCjmsZCOZ-EnT03XdLpOGD7JJuTY390gSwnLDyUrcANh5Ee7vQslhX_JoW21X6zahtjD5av7AdFODis28FFUvoEVpVA6YF1GBNWnWZM4NW7pLB80qC_e55YM8A94KwCO4XgFZIb7WtccIpaMxe-0Z7xqr4Jvb3rRQ7is9aw7duIJJ8VbMJNn3PYX8SExGDj_v8KXMsfES378XWlNxrDOvPsuGOffHd3ZbEYcgz8cuhQA/https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttps-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer%26d%3DDwMGaQ%26c%3DJeTkUgVztGMmhKYjxsy2rfoWYibK1YmxXez1G3oNStg%26r%3DsgvCAzCi3iTXkTNRRVMpDnC6tu0lnijYpKXIX_UNme8%26m%3DfpoXixpvd3xg4zKFCneh4htkD8tY1AMVOBy-oFTzowE%26s%3DGQ9WiCjvjOKMafL9Hpx2p-I-IxfulNIgIZoX68MXWVk%26e%3D > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > > > > https://secure-web.cisco.com/1BHPyB8CIVSzr5IgeDfAEXJjqATyG9e6kVhL_t7upizzcjnjT36yptmbyKlP1rrMolxNrsgSuyFFuDZpwJwzmHWYOwbzZ2bPvcDEFqwJeTerGFh7A6_kvBYc8rHRcSm2MxzBIsRwA0oBT5SVBTfDyrw4ELuoMhy7W92aF-ycnw-w2nHxRbyqi_ONn_E2NaSvxto0XykYz6sE79AnOWkMaAB5fuRskTBa_VN3fNxr4zI8_B8ircBkuimaE7L-gGyyX6BQ2z4qcYNqAquKMRh__ZA/https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttps-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer%26d%3DDwICAg%26c%3DJeTkUgVztGMmhKYjxsy2rfoWYibK1YmxXez1G3oNStg%26r%3DsgvCAzCi3iTXkTNRRVMpDnC6tu0lnijYpKXIX_UNme8%26m%3DfpoXixpvd3xg4zKFCneh4htkD8tY1AMVOBy-oFTzowE%26s%3DGQ9WiCjvjOKMafL9Hpx2p-I-IxfulNIgIZoX68MXWVk%26e%3D > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://secure-web.cisco.com/1KbZja1ax8QeWP1rZenlThlm3sXldMmQDaueJm2WzKtxhcva3HXAYZUBqF_VIlM798BYr2erwyDgh2oK6r2_kznhgI-vezVLn-OLoAxqzXE_LzNtjN7G0RyTCa2d9042DMQXrtjjHcMLxXRIG-9zeQYJPzUsQ20qHOKNwIElXJEy1kprzAbXr9jMYLSSeoFCSlDlAV-PgMKMlS2mIY6DGW-B48xoyVqPGCuzsclowspTLFd4whVzRi54vNMF7d44nbqQ4ooNaNMVm4iKqnDfxcQ/http%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fpipermail%2Ffreesurfer%2Fattachments%2F20201217%2F6534ca05%2Fattachment-0001.html > > ------------------------------ > > Message: 7 > Date: Thu, 17 Dec 2020 14:40:57 +0000 > From: "Greve, Douglas N.,Ph.D." <dgr...@mgh.harvard.edu> > Subject: Re: [Freesurfer] group analyses {Disarmed} > To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu> > Message-ID: <8ede4058-1020-1a32-398a-0e44a37a1...@mgh.harvard.edu> > Content-Type: text/plain; charset="utf-8" > > If you want to apply etiv correction when extracting the cortical volume > with mris_preproc, just add --etiv to the command > > On 12/14/2020 9:59 AM, Sara Lyn wrote: > > External Email - Use Caution > > Hi > Thank you for your response. How do I correct this extracted volume for > intracranial volume (etiv)? > > Thank you > > Sara > > On Sun, Dec 13, 2020 at 12:30 PM Greve, Douglas N.,Ph.D. < > dgr...@mgh.harvard.edu<mailto:dgr...@mgh.harvard.edu>> wrote: > When you run the thickness analysis with multiple comparisons correction > (mri_glmfit-sim), it will create "ocn" files. These will be clusters of the > significant areas. You can use this to extract other information. If you > want volume, then run mris_preproc using the --meas volume flag, the apply > the ocn to this file using mri_segstats using the --avgwf and --accumulate > flags (and --exclude 0). This will give you a nsubjects-by-nclusters text > file where each entry is the volume for that subject/cluster > > On 12/8/2020 10:48 AM, Sara Lyn wrote: > > External Email - Use Caution > > Hi Joceyln, > > I'm not trying to run a new group analysis but want to extract volume > values from significant thickness ROIs obtained from a thickness group > analysis. > > Thank you > > Sara > > On Tue, Dec 8, 2020 at 10:38 AM Mora, Jocelyn S. <jsm...@mgh.harvard.edu > <mailto:jsm...@mgh.harvard.edu>> wrote: > Hi Sara, > > You may want to try --meas volume in place of --meas thickness when > running mris_preproc. > > I would also recommend looking at our ROI Analysis< > https://secure-web.cisco.com/1g2kRJfau7HjSgmWu9k1y2XTwIMcBGIA-XwH0H7VI8zAxTQzb4aOSMDp6R8Jfi0Po3NMRSG9C0LtNtm6-woQEgwl-cwbWL8_TXyPMqoIvev2Gk5xKmwgW8IuFaQjw69Y3FCuRKwDVHOMSTjPP3MAi29ARxwq_LRpLO7bxtHZW1jAyuRNtrmD4erpddTzuHg3F62ADZRqOYBLyWHlzBBPqp7yCdVoH4o7Gia01u1hT-aoNc8JHUlKMud7cMQz4MsOZAOv64wbXgkh8bAUP0bhvAg/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FAnatomicalROIV6.0> > tutorial and Volumetric Group Analysis< > https://secure-web.cisco.com/1tHYiEwJMSx00y8RdQYJIg0nUV5bkFIzrk567zMxayemPQ09G48rqDnWqw4E6yrlMBJLktsyeyMdqA8GdbPJDzXQF7xx_UyMd7vKwH4Re9TF4tJdv1FaNzemfK7i5QI7Psfkt891h5PytK7i7KSod464UAFFriIC4NrIYk_lzZGh6ljc-y-Q3jIxXf0RbP6lDllgUJaJ3XS9i_BCSUoZAUhpAyzrfLoi1XWxtXjxQl_iCBoocEJOpE_SFyFHLaZYUyWgGShrqcIZTYr-w7rqWSQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FVolumetricGroupAnalysis%3Fhighlight%3D%2528thickness%2529%257C%2528volume%2529%257C%2528measure%2529> > tutorial. Please let us know if you are > still having trouble. > > Cheers, > Jocelyn > ________________________________ > From: freesurfer-boun...@nmr.mgh.harvard.edu<mailto: > freesurfer-boun...@nmr.mgh.harvard.edu> < > freesurfer-boun...@nmr.mgh.harvard.edu<mailto: > freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of Sara Lyn < > saralyn...@gmail.com<mailto:saralyn...@gmail.com>> > Sent: Monday, December 7, 2020 10:43 AM > To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu<mailto: > freesurfer@nmr.mgh.harvard.edu>> > Subject: [Freesurfer] group analyses > > > External Email - Use Caution > > Hi FS developers, > > I ran mris_preproc, surf2 surf and glmfit and cluster analyses (monte > carlo) for a surface based thickness group analysis. I am trying to extract > volume measures from the same significant thickness ROIs. Is there any way > to do this? Thank you! > > Sara > _______________________________________________ > Freesurfer mailing list > 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 > https://secure-web.cisco.com/1d5gSB-rqVInM6onHMLDbLhUREGgzCvmI5zHvbuwq-S_PJCuw3EMc2kV4eq7chGX405ndWxjVJST5a2MbctIecDLR4jHj04tzIjlJ-K7sRsBSXoEHazGQR-uVM6rudDyR3Y7AQdBZKN8dtBn7OKIjFZVtUqZrOpgRSs_YB6U1oRHHI1srOBKZMXCRbkMkqN4s6POAVqoNSpgM_OA-E6E20iqNg7LlTqjMfc_o7LATYKEK3dYGTrk8OoLqWVwO9U3mBsRw9E6-T1zhH7qaRm4vJA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer< > https://secure-web.cisco.com/1R7gYfs8YU2juqb8rGfBqpwv3CspfKQQgYn6WAikOwc_TDtnxjDjMy1r78KDcMil_IHVde58fWtF5nHDeV6y8sFImL3Jlld9a57iSW_DaW4BFEV6cg_YjqRNhnbaF-4ZaZFCs50k7MRt2-YvVF4mZuaP6kh5g9RnM5y_TMYZJm0LyS8ruzjLF6IgU9yMOHVXmVHUWva7T8KfHrZiljMRns81fwr4TsXqvlnzXZDMISe0Rk2ANRklyDOi8QKTcN8ierog6gWIQQPYLNQce_Kn_gw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer > > > > > > _______________________________________________ > Freesurfer mailing list > 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 > https://secure-web.cisco.com/1d5gSB-rqVInM6onHMLDbLhUREGgzCvmI5zHvbuwq-S_PJCuw3EMc2kV4eq7chGX405ndWxjVJST5a2MbctIecDLR4jHj04tzIjlJ-K7sRsBSXoEHazGQR-uVM6rudDyR3Y7AQdBZKN8dtBn7OKIjFZVtUqZrOpgRSs_YB6U1oRHHI1srOBKZMXCRbkMkqN4s6POAVqoNSpgM_OA-E6E20iqNg7LlTqjMfc_o7LATYKEK3dYGTrk8OoLqWVwO9U3mBsRw9E6-T1zhH7qaRm4vJA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer< > https://secure-web.cisco.com/1Ah2pQDy0yVPBrfOlJQCt09VXbFckNrCLFlfFNhGHNiCLlihCT3a6Ao1ukmi54Op5WeEN28uVon2Aa_HTqcoHfEdsl_re_L0spoNerp7ipV9SBML8-Q3TGejLNOFiCik56W4gG1pbAWG_X1hi5bEiosvdOAY-lEqJpt5S0y7GXEuii4ROjgqTz8VOufJkTAi4noM8xExAhDNJ7pHx9On1nmsWsG2uGmkUMr-a0lvO1xexIN4H4GW4jke_tb9H5_AdIqrFbjW7k_1RzaJhTHezvg/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer > > > > _______________________________________________ > Freesurfer mailing list > 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 > https://secure-web.cisco.com/1d5gSB-rqVInM6onHMLDbLhUREGgzCvmI5zHvbuwq-S_PJCuw3EMc2kV4eq7chGX405ndWxjVJST5a2MbctIecDLR4jHj04tzIjlJ-K7sRsBSXoEHazGQR-uVM6rudDyR3Y7AQdBZKN8dtBn7OKIjFZVtUqZrOpgRSs_YB6U1oRHHI1srOBKZMXCRbkMkqN4s6POAVqoNSpgM_OA-E6E20iqNg7LlTqjMfc_o7LATYKEK3dYGTrk8OoLqWVwO9U3mBsRw9E6-T1zhH7qaRm4vJA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer< > https://secure-web.cisco.com/1Ah2pQDy0yVPBrfOlJQCt09VXbFckNrCLFlfFNhGHNiCLlihCT3a6Ao1ukmi54Op5WeEN28uVon2Aa_HTqcoHfEdsl_re_L0spoNerp7ipV9SBML8-Q3TGejLNOFiCik56W4gG1pbAWG_X1hi5bEiosvdOAY-lEqJpt5S0y7GXEuii4ROjgqTz8VOufJkTAi4noM8xExAhDNJ7pHx9On1nmsWsG2uGmkUMr-a0lvO1xexIN4H4GW4jke_tb9H5_AdIqrFbjW7k_1RzaJhTHezvg/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer > > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> > https://secure-web.cisco.com/1d5gSB-rqVInM6onHMLDbLhUREGgzCvmI5zHvbuwq-S_PJCuw3EMc2kV4eq7chGX405ndWxjVJST5a2MbctIecDLR4jHj04tzIjlJ-K7sRsBSXoEHazGQR-uVM6rudDyR3Y7AQdBZKN8dtBn7OKIjFZVtUqZrOpgRSs_YB6U1oRHHI1srOBKZMXCRbkMkqN4s6POAVqoNSpgM_OA-E6E20iqNg7LlTqjMfc_o7LATYKEK3dYGTrk8OoLqWVwO9U3mBsRw9E6-T1zhH7qaRm4vJA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://secure-web.cisco.com/1-eTgd8c2t6kIrc4hMnU_VeSZs1MY0xAD0QPks_BUpHMiuLXOQuGhnI_Pgs3gGP3p5wr4cWhSu1L8DM-ILClxBJLnIFkxYxMivHxpKi66bRgoP9vK3LN2mCSYHFfm2x6jtz4KubvYLgoUhhHEU5YkSHzT8JtrugKAYtSwkQ2k8oIa5yJ-OCUjHjafrHZK8oawszfjQm8fMPZ4UP9wNLwMD-PKDwH8RH9mO6hSKJByH7U4hgb3rJqeuZEtBQrARviXWcMcl_YKgdEzg9UHILW3dg/http%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fpipermail%2Ffreesurfer%2Fattachments%2F20201217%2F3b93cc0b%2Fattachment.html > > ------------------------------ > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://secure-web.cisco.com/1d5gSB-rqVInM6onHMLDbLhUREGgzCvmI5zHvbuwq-S_PJCuw3EMc2kV4eq7chGX405ndWxjVJST5a2MbctIecDLR4jHj04tzIjlJ-K7sRsBSXoEHazGQR-uVM6rudDyR3Y7AQdBZKN8dtBn7OKIjFZVtUqZrOpgRSs_YB6U1oRHHI1srOBKZMXCRbkMkqN4s6POAVqoNSpgM_OA-E6E20iqNg7LlTqjMfc_o7LATYKEK3dYGTrk8OoLqWVwO9U3mBsRw9E6-T1zhH7qaRm4vJA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer > > End of Freesurfer Digest, Vol 202, Issue 30 > ******************************************* >
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