[Freesurfer] recon-all error with T1 dcm images
External Email - Use Caution Hi, Dear Freesurfer experts I'm have met a recon-all errors with data collected recently like this ADNI_002_S_6652_MR_Accelerated_Sagittal_MPRAGE__br_raw_20190122095958285_147_S786989_I1118713.dcm The attachments are the recon-all script and the output log. Can you help me with this? Thanks Best, Wei recon-all.log Description: Binary data module load nixpkgs/16.09 module load freesurfer/7.1.0 source $EBROOTFREESURFER/FreeSurferEnv.sh export SUBJECTS_DIR=/home/weishao/scratch/ADNI-MCI/subjects recon-all -all -i /home/weishao/scratch/ADNI-MCI/ADNI/032_S_6652/Accelerated_Sagittal_MPRAGE/2019-06-07_09_08_48.0/I1174541/ADNI_032_S_6652_MR_Accelerated_Sagittal_MPRAGE__br_raw_20190610135118632_19_S831455_I1174541.dcm \ -s S6652 -openmp 32 echo "job is done" ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] hippocampal subfield segmentation with DCM
External Email - Use Caution Hi, FreeSurfer experts I'm wondering if there is a way to do hippocampal subfield segmentation with T2 DCM images, instead of NifTi. like this ADNI_002_S_0295_MR_Axial_T2-Star__br_raw_20110602125226394_36_S110471_I238619.dcm Best, Wei ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] same ROI with different stats
External Email - Use Caution Hi, Freesurfer exports I'm wondering what is the difference in the stat folder when it comes to the same ROI. For example, I have found the entorhinal from 4 different stats files and the values are slightly different. lh.aparc.DKTatlas.stats entorhinal665393 1528 3.174 0.788 0.085 0.021 5 0.5 lh.aparc.pial.stats entorhinal848799 1906 3.159 0.787 0.199 0.068 16 3.1 lh.BA_exvivo.stats entorhinal_exvivo570346 1394 3.000 1.015 0.083 0.023 5 0.4 lh.BA_exvivo.thresh.stats entorhinal_exvivo344205918 3.450 0.520 0.057 0.010 1 0.1 I‘m really appreciate it if you can provide me some instructions about these 4 Best, Wei ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Question about mri_info
External Email - Use Caution Hello, Freesurfer exports My name is Wei Shao, I'm a beginner at Freesuefer and curious about the mri_info. I have searched the information through freesurfer online documents but there is not much I can find. I'm wondering are there any supplement documents that can explain each term of this information such as fov, dof, and frames and so on? [image: MRI_info.PNG] Best, Wei ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Question about hippocampal sub-volume extraction
External Email - Use Caution Hello, there I just want to follow up on this question, is there any command that I can use to extract the T2 sub-volume from two different groups of subjects(AVP and BAY) of the hippocampus from Freesurfer? Best, Wei On Mon, May 3, 2021 at 8:13 PM Wei Shao wrote: > Hi, Abdalla Z Mohamed > > Thanks for your reply, but this is code is for T1 scan only according to > the instruction, I want to extract the volume from the T2 (for segmentation > based only on the additional scan ) > > Best, > Wei > > On Mon, May 3, 2021 at 7:55 PM wrote: > >> External Email - Use Caution >> >> Hi Wei, >> >> You can directly extract the volumes from all subjects within your >> Freesurfer Analysis folder by using the following command >> >> quantifyHAsubregions.sh hippoSf T1 result.txt >> >> >> >> Best regards, >> >> Abdalla Z Mohamed. >> >> >> >> >> >> *From: *Wei Shao >> *Sent: *Tuesday, 4 May 2021 5:22 AM >> *To: *Freesurfer support list >> *Subject: *[Freesurfer] Question about hippocampal sub-volume extraction >> >> >> >> *External Email - Use Caution* >> >> Hello,Dear Freesurfer exports >> >> >> >> I have a question about the pipeline of hippocampal sub-volume extraction: >> >> quantifyHAsubregions.sh hippoSf - >> >> >> Let's say I have two different groups of analysisID such as sub-AVP >> and sub-BAY >> >> >> >> I can pass a wildcard to extract the data of T2 scan from all sub-BAY >> subjects by quantifyHAsubregions.sh hippoSf BAY*-T2 result.txt >> >> >> >> But Is there any way that I can extract the sub-volume from all the two >> different group subjects at one time? Thanks. >> >> >> >> Best, >> >> Wei >> >> >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://secure-web.cisco.com/1_qQQO5si0e7EycOopl3CxbFa3PGptFQTAh5fiudLIjknANTmaHRI29rSaPBSrWhAjhVRNgRxIbmCKfSeRA2zurxj7xVRnneV35OyfshqN311mX99zv8TEiD-HWXZOWRXP10cKEFUndjM0KiBgb5W_vwJjfxiDYU6-HjfGP6ikPhUWhgxduxxzy1ke9_cCMhS5gzOgg6lVQpwrpOtKaf3fYU5YVUJKZa829APxjMyjW11bZcZH61ez3zZS2NVnCddZ4pl3WjNh60coHQyAL9_8Q/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Question about hippocampal sub-volume extraction
External Email - Use Caution Hi, Abdalla Z Mohamed Thanks for your reply, but this is code is for T1 scan only according to the instruction, I want to extract the volume from the T2 (for segmentation based only on the additional scan ) Best, Wei On Mon, May 3, 2021 at 7:55 PM wrote: > External Email - Use Caution > > Hi Wei, > > You can directly extract the volumes from all subjects within your > Freesurfer Analysis folder by using the following command > > quantifyHAsubregions.sh hippoSf T1 result.txt > > > > Best regards, > > Abdalla Z Mohamed. > > > > > > *From: *Wei Shao > *Sent: *Tuesday, 4 May 2021 5:22 AM > *To: *Freesurfer support list > *Subject: *[Freesurfer] Question about hippocampal sub-volume extraction > > > > *External Email - Use Caution* > > Hello,Dear Freesurfer exports > > > > I have a question about the pipeline of hippocampal sub-volume extraction: > > quantifyHAsubregions.sh hippoSf - > > > Let's say I have two different groups of analysisID such as sub-AVP > and sub-BAY > > > > I can pass a wildcard to extract the data of T2 scan from all sub-BAY > subjects by quantifyHAsubregions.sh hippoSf BAY*-T2 result.txt > > > > But Is there any way that I can extract the sub-volume from all the two > different group subjects at one time? Thanks. > > > > Best, > > Wei > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://secure-web.cisco.com/1ElFYk2W8crrhUek2tE-Mwm4-KKwBJnP7zRoOg--stEzWjkabm39zKvzlC7c2JLgfxaqDrZLJaC0s36qEXjzlV9iG2l_iQ5hnGbv2TsArJc7gETdY7zIqmW2DbabVT-wC14t7udnhdQYmYc1YSZQuE8zOvbwc6KK3rCE2kTocmhSQ1JVQTGjm68xA6KFku9a_nnfeHr2gYD8KVS6iA8W8vwONMObizCEhX7Teknr6lHQ8VH23h1EgQp6SvdEcCKFU8Xmjs6lH1dNM2f16GT04XQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Question about hippocampal sub-volume extraction
External Email - Use Caution Hello,Dear Freesurfer exports I have a question about the pipeline of hippocampal sub-volume extraction: quantifyHAsubregions.sh hippoSf - Let's say I have two different groups of analysisID such as sub-AVP and sub-BAY I can pass a wildcard to extract the data of T2 scan from all sub-BAY subjects by quantifyHAsubregions.sh hippoSf BAY*-T2 result.txt But Is there any way that I can extract the sub-volume from all the two different group subjects at one time? Thanks. Best, Wei ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Out of memory from longitudinal segmentation of hippocampus
External Email - Use Caution Hi, E Thanks for your reply, I used one core and its associated RAM from the server,(I guess is not very much) but I have solved it by assigning more RAM memory. Best, Wei On Fri, Apr 30, 2021 at 9:35 AM Iglesias Gonzalez, Juan E. < jiglesiasgonza...@mgh.harvard.edu> wrote: > Dear Wei, > > Sorry for missing your message (it happens sometimes…). > > The longitudinal subfield module is very RAM memory hungry. > > How much RAM memory do you have (not disk space, these are different > things). > > Cheers, > > /Eugenio > > > > > > > > > > > > > > Juan Eugenio Iglesias > > Senior research fellow > > CMIC (UCL), MGH (HMS) and CSAIL (MIT) > > http://secure-web.cisco.com/1tjk3OL0B6Drsa3xCXMNVuI8sfeKEW4_XP4tWvrd_ajd5F67eazolqhGpHBgeo1L5gH3VYBePfywpla8y2ELEjhHj1D_-3_bryJu2GGFeyDr4m-hTdINqzbyWpmow9_PjNYF_DqMZlL3XYdJBbhnPCzF1vNFprQS0wyIi3mkq--Hd5NeqhDQeCl6ARiRfGOVFCxYDP9144ghi_gvC_eFPX_NN0eEYiK4ddz8MNB3EFMEj7YGCYWJC3Zh9V7kKMIVVAwuETkeZx9JyiEy1lCxeXg/http%3A%2F%2Fwww.jeiglesias.com > > > > > > > > *From: * on behalf of Wei Shao < > ws...@research.baycrest.org> > *Reply-To: *Freesurfer support list > *Date: *Thursday, April 29, 2021 at 22:39 > *To: *Freesurfer support list > *Subject: *Re: [Freesurfer] Out of memory from longitudinal segmentation > of hippocampus > > > > *External Email - Use Caution* > > Hello, Dear Freesufer experts > > > > I just thought of sending a friendly reminder - > > > > I am wondering if you had the time to go over my question? > > > > Best regards, > > Wei > > > > On Sat, Apr 24, 2021 at 2:26 PM Wei Shao > wrote: > > Hello, Dear FreeSurfer expert. > > > > I was tried to use longitudinal segmentation of T1 scans for the > longitudinal analysis. but there is a problem > > > > making Unknown map to reduced label 13 > > Computing hyperparameters for estimation of Gaussian parameters > > Error using permute > > Out of memory. Type HELP MEMORY for your options. > > > > Error in myMRIread>myMRIread_aux (line 99) > > Error in myMRIread (line 63) > > Error in SegmentSubfieldsT1Longitudinal (line 904) > > > > MATLAB:nomem > > @#@FSTIME 2021:04:24:13:57:21 run_SegmentSubfieldsT1Longitudinal.sh N 17 > e 249.25 S 49.95 U 759.76 P 324% M 1532492 F 249 R 4682496 W 0 c 134624 w > 550491 I 3940880 O 1217536 L 1.24 1.04 1.58 > > @#@FSLOADPOST 2021:04:24:14:01:30 run_SegmentSubfieldsT1Longitudinal.sh N > 17 4.04 3.43 2.47 > > Linux gra-login1 3.10.0-1127.8.2.el7.x86_64 #1 SMP Tue May 12 16:57:42 UTC > 2020 x86_64 GNU/Linux > > > > longitudinal subfields exited with ERRORS at Sat Apr 24 14:01:31 EDT 2021 > > > > For more details, see the log file > /home/weishao/long_BAY12019/scripts/long-hippocampal-subfields-T1.log > > > > I have checked the space: > > > > DescriptionSpace # of > files > > /home (user weishao) 44G/53G > 147k/500k > > > > Could you tell me what I should do? Thanks > > > > Best, > > Cheer > > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://secure-web.cisco.com/10s0rSGqrMXf8pbGw-apOZS8Sg6FOJ6-pc03S7idFntcgyXeYQQYiBkDhzKzXWmPxmNe6XdZll94CEpSzbmJUaaqXrYxNj85rgVkBVTvQkiXE2Mxn134omXkoYW9_r6Z2YZH6CyVPns5gnKRBZOMTCyYPnUPhxyBFFacyzPm1MvaBHhKNUQxizaT91VeFEPieAhMJpNozAtKoBb411NnjQarHj41mXuKKHfKJnxJ6hzbzpSViIJwWeknFAkpqVGHw16VFvz6kjvFprnS1GA-neg/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer > The information in this e-mail is intended only for the person to whom it > is addressed. If you believe this e-mail was sent to you in error and the > e-mail contains patient information, please contact the Mass General > Brigham Compliance HelpLine at > http://secure-web.cisco.com/1jDzOMD5Myk0I2qKSVVd8C-L7Y_Er3jFaTeA93UhgUM_reWbWCCYTm7K7OvZtBrXGwaKeehNZg23E814GYZuf47rf3wMR0aMjBIflRuhynQU_nw5Qx8e14QXaPi6wPlIXiXxEfwC5fSWK8fR6LhF8351Vl96nwjj0_JlK6DAruwvXkL905hSmcaeM_f6GsFeWLAjtS_57pkBhhDww15LC_DRSAjJdpC8Z9NsV7NUndlYZ1rla8iemcMJ-mtQAlPRHDmMsuXibsXuZcT1-WnKeiw/http%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline > . If the e-mail was sent > to you in error but does not contain patient information, please contact > the sender and properly dispose of the e-mail. > Please note that this e-mail is not secure (encrypted). If you do not > wish to continue communication over unencrypted e-mail, please notify the > sender of this message immediately. Continuing to send or respond to > e-mail after receiving this message means you understand and accept this > risk and wish to continue to communicate over unencrypted e-mail. > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Out of memory from longitudinal segmentation of hippocampus
External Email - Use Caution Hello, Dear Freesufer experts I just thought of sending a friendly reminder - I am wondering if you had the time to go over my question? Best regards, Wei On Sat, Apr 24, 2021 at 2:26 PM Wei Shao wrote: > Hello, Dear FreeSurfer expert. > > I was tried to use longitudinal segmentation of T1 scans for the > longitudinal analysis. but there is a problem > > making Unknown map to reduced label 13 > Computing hyperparameters for estimation of Gaussian parameters > Error using permute > Out of memory. Type HELP MEMORY for your options. > > Error in myMRIread>myMRIread_aux (line 99) > Error in myMRIread (line 63) > Error in SegmentSubfieldsT1Longitudinal (line 904) > > MATLAB:nomem > @#@FSTIME 2021:04:24:13:57:21 run_SegmentSubfieldsT1Longitudinal.sh N 17 > e 249.25 S 49.95 U 759.76 P 324% M 1532492 F 249 R 4682496 W 0 c 134624 w > 550491 I 3940880 O 1217536 L 1.24 1.04 1.58 > @#@FSLOADPOST 2021:04:24:14:01:30 run_SegmentSubfieldsT1Longitudinal.sh N > 17 4.04 3.43 2.47 > Linux gra-login1 3.10.0-1127.8.2.el7.x86_64 #1 SMP Tue May 12 16:57:42 UTC > 2020 x86_64 GNU/Linux > > longitudinal subfields exited with ERRORS at Sat Apr 24 14:01:31 EDT 2021 > > For more details, see the log file > /home/weishao/long_BAY12019/scripts/long-hippocampal-subfields-T1.log > > I have checked the space: > > DescriptionSpace # of > files > /home (user weishao) 44G/53G > 147k/500k > > Could you tell me what I should do? Thanks > > Best, > Cheer > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Hippocampus segmentHA_T1.sh
External Email - Use Caution HI, E I was take the wrong directory, Sorry for the mistake. Cheer, Wei > On Apr 23, 2021, at 1:28 PM, Iglesias Gonzalez, Juan E. > wrote: > > Shouldn’t it be segmentHA_T1.sh 01 instead of segmentHA_T1.sh sub-01 ? > > > Juan Eugenio Iglesias > Senior research fellow > CMIC (UCL), MGH (HMS) and CSAIL (MIT) > http://secure-web.cisco.com/1Nx7i4KGm6MOshYnOV8FIIKnbW9fVxXk8H5ZhGy1mQM7_aYahNIlsMfwPiz_aOg66PN9tJJ9sgBLG-Rfyc7_c_5zlzt9HSe6FQ-s6Y8C0jk9Agmli1n66vWaLc8KtWoq5Spimyf3cvCoMlOX3vgsicAglCjYyXMpxOj010GJnsOVAvyQDB0X-JM2aCc6jW6VAZ9BLabpFbU0NojSnNvgf_7-pIT64E5zfwYzHthaDoeocfJtsnn848TqyOsgP-xZB/http%3A%2F%2Fwww.jeiglesias.com > > <http://secure-web.cisco.com/19iAjCpC9PU480UGjXtraLpCYYlGzPse5r5gRi3QNJB8z34CBG6P2-8NEDc9BTmOf9nAsrHutxAiMjIrFRYYoEQ7zd5DUfDNznJqpKfpLOeChJd_R51eU9e--t3niP5Hhka7Lo0pX-fe2Nv2KNybVKmFTDsXhMSMc61QLjeLbGB19VGSQY_-n7WwsHcbxgofEBaih1GYKDl7i1eeeXcxmXiZdg14BdnP2OuUEAUR8y_jxKmQ1jvk-H9L6w4OAWybg/http%3A%2F%2Fwww.jeiglesias.com%2F> > > > > > From: <mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of Wei Shao > mailto:ws...@research.baycrest.org>> > Reply-To: Freesurfer support list <mailto:freesurfer@nmr.mgh.harvard.edu>> > Date: Friday, April 23, 2021 at 12:04 > To: Freesurfer support list <mailto:freesurfer@nmr.mgh.harvard.edu>> > Subject: Re: [Freesurfer] Hippocampus segmentHA_T1.sh > > External Email - Use Caution > Hi, E > > [weishao@gra-login1 01]$ find . -name "talairach.xfm" > ./mri/transforms/talairach.xfm > > module load freesurfer/7.1.0 > > export SUBJECTS_DIR=/home/weishao/scratch/BART > > segmentHA_T1.sh sub-01 > > Best, > Wei > > On Fri, Apr 23, 2021 at 11:35 AM Iglesias Gonzalez, Juan E. > <mailto:jiglesiasgonza...@mgh.harvard.edu>> wrote: >> I’m assuming transforms/talairach.xfm is in there? >> Also: what was the exact command you ran? >> Cheers, >> /E >> >> 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 >> http://secure-web.cisco.com/1Nx7i4KGm6MOshYnOV8FIIKnbW9fVxXk8H5ZhGy1mQM7_aYahNIlsMfwPiz_aOg66PN9tJJ9sgBLG-Rfyc7_c_5zlzt9HSe6FQ-s6Y8C0jk9Agmli1n66vWaLc8KtWoq5Spimyf3cvCoMlOX3vgsicAglCjYyXMpxOj010GJnsOVAvyQDB0X-JM2aCc6jW6VAZ9BLabpFbU0NojSnNvgf_7-pIT64E5zfwYzHthaDoeocfJtsnn848TqyOsgP-xZB/http%3A%2F%2Fwww.jeiglesias.com >> >> <http://secure-web.cisco.com/1Z77TacJkkAC58QyArzEVJDV_7X8Igro89XsggKNL0YRV39s2J3KnuYhyDYqdablT7K4waWew1NMuAm_1jfuvKuLUFGGcPObl7Lba56vs7bE-yV8BNN5sW4jWmKDYBCaTCHJKMt7IBlZicKoh235BDGiCfWiezwX2kIvAS3UlIuvd4PN_IFqc2iowh312LHnHDCQ53ea1gSk4H3Th6VAJ2NXlBvJM9qaLDKyFd02VgXiETYyw2tNFfN3h2cuLMizK/http%3A%2F%2Fwww.jeiglesias.com> >> >> >> >> >> From: > <mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of Wei Shao >> mailto:ws...@research.baycrest.org>> >> Reply-To: Freesurfer support list > <mailto:freesurfer@nmr.mgh.harvard.edu>> >> Date: Friday, April 23, 2021 at 11:05 >> To: Freesurfer support list > <mailto:freesurfer@nmr.mgh.harvard.edu>> >> Subject: [Freesurfer] Hippocampus segmentHA_T1.sh >> >> External Email - Use Caution >> Hello, Dear FreeSurfer expert >> >> I tried to use segmentHA_T1.sh for the hippocampus subfields, However, here >> is the log >> cannot find the wmparc.mgz or norm.mgz or talairach.xfm for the subject. >> Has the subject been procesed with recon-all? >> >> But the wmparc.mgz and norm.mgz are there >> >> >> >> Could you tell me how to fix this? Thanks! >> >> Best, >> Wei >> >> >> ___ >> 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/16U9haZBIQwQFBcRT0cXF1WactZcnPPhgGdaRUvvpaa4FhvMGk4CrAUdiloycOyHcWYr3uTIhk62Aw0gdWh_5PXprPztpo-T_el_mbKSgLwTpVkAakSZSRY734Nw3Dl3oTpvnNYdCMVc2CCCPq7QpaWmnYLEmaTXCxkjSbtWIehnxi3cgbq7NcTwT46Q0wm6HMAaQuuxyeaEECtAmk1Mzuz3YyDIYVU0S9klruI5eEGF9LwQOzaZLb7KZ7tVgdEo2q7Hu8MZJw87vw8KfZNP9KQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer >> >> <https://secure-web.cisco.com/1Eun7W78BTcuyipDrWGIHKg_NsRuLOs4GO-ZrOtIG85OkXlVvZp6IvEwebF-EGHJLvKIxHkJxnrwA_ONMIv2lBS9Uv6DfnOuoxau-7DLGGrh-lPryxy4mjeHeT8fq8_CcnPObzoEJ54iSEpSV82HrEAw
Re: [Freesurfer] Hippocampus segmentHA_T1.sh
External Email - Use Caution Hi, E [weishao@gra-login1 01]$ find . -name "talairach.xfm" ./mri/transforms/talairach.xfm module load freesurfer/7.1.0 export SUBJECTS_DIR=/home/weishao/scratch/BART segmentHA_T1.sh sub-01 Best, Wei On Fri, Apr 23, 2021 at 11:35 AM Iglesias Gonzalez, Juan E. < jiglesiasgonza...@mgh.harvard.edu> wrote: > I’m assuming transforms/talairach.xfm is in there? > > Also: what was the exact command you ran? > > Cheers, > > /E > > > > Juan Eugenio Iglesias > > Senior research fellow > > CMIC (UCL), MGH (HMS) and CSAIL (MIT) > > http://secure-web.cisco.com/1Z77TacJkkAC58QyArzEVJDV_7X8Igro89XsggKNL0YRV39s2J3KnuYhyDYqdablT7K4waWew1NMuAm_1jfuvKuLUFGGcPObl7Lba56vs7bE-yV8BNN5sW4jWmKDYBCaTCHJKMt7IBlZicKoh235BDGiCfWiezwX2kIvAS3UlIuvd4PN_IFqc2iowh312LHnHDCQ53ea1gSk4H3Th6VAJ2NXlBvJM9qaLDKyFd02VgXiETYyw2tNFfN3h2cuLMizK/http%3A%2F%2Fwww.jeiglesias.com > > > > > > > > *From: * on behalf of Wei Shao < > ws...@research.baycrest.org> > *Reply-To: *Freesurfer support list > *Date: *Friday, April 23, 2021 at 11:05 > *To: *Freesurfer support list > *Subject: *[Freesurfer] Hippocampus segmentHA_T1.sh > > > > *External Email - Use Caution* > > Hello, Dear FreeSurfer expert > > > > I tried to use segmentHA_T1.sh for the hippocampus subfields, However, > here is the log > > cannot find the wmparc.mgz or norm.mgz or talairach.xfm for the subject. > > Has the subject been procesed with recon-all? > > > > But the wmparc.mgz and norm.mgz are there > > > > > > Could you tell me how to fix this? Thanks! > > > > Best, > > Wei > > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://secure-web.cisco.com/1Eun7W78BTcuyipDrWGIHKg_NsRuLOs4GO-ZrOtIG85OkXlVvZp6IvEwebF-EGHJLvKIxHkJxnrwA_ONMIv2lBS9Uv6DfnOuoxau-7DLGGrh-lPryxy4mjeHeT8fq8_CcnPObzoEJ54iSEpSV82HrEAwcsKHXm6hb3ujhqSpIhtSD03rFye6w6J7AEE8CETP8TO-ZXpupek_V0diqnrkXehUXvZXkMXJjS0U5M3QqBdE0pJGJPH56uDEDZA7K7I-9qazuodoH5LVNYDEp5fNaZA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer > The information in this e-mail is intended only for the person to whom it > is addressed. If you believe this e-mail was sent to you in error and the > e-mail contains patient information, please contact the Mass General > Brigham Compliance HelpLine at > http://secure-web.cisco.com/11U8xUR8f2441jEGJ416m8uVq2qAjxEg-du5tbVs-2MtTwWq2aNhcq-emUFiCBDrE3ZYHesqFglrfnz6hVZWCj9jGIKgXvEEDwHTGsappvPN3pj9A6h7Fp-0PlYtKv7iJKDiXnHDmt2YNzNm34SvHO1-dNilTh85M1TgLD8X5fO2aKLcUgcP8zxmPU21jYFb-AXvxRqzdwlJ1bOC8Gm2t4mzfznlD55tbEIhtbLCjJm0KFkQDvsm8p0PnpFbmyRjiv9PNOiaCWCwT8nXMae3MQw/http%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline > . If the e-mail was sent > to you in error but does not contain patient information, please contact > the sender and properly dispose of the e-mail. > Please note that this e-mail is not secure (encrypted). If you do not > wish to continue communication over unencrypted e-mail, please notify the > sender of this message immediately. Continuing to send or respond to > e-mail after receiving this message means you understand and accept this > risk and wish to continue to communicate over unencrypted e-mail. > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Hippocampus segmentHA_T1.sh
External Email - Use Caution Hello, Dear FreeSurfer expert I tried to use segmentHA_T1.sh for the hippocampus subfields, However, here is the log cannot find the wmparc.mgz or norm.mgz or talairach.xfm for the subject. Has the subject been procesed with recon-all? But the wmparc.mgz and norm.mgz are there [image: Capture.PNG] Could you tell me how to fix this? Thanks! Best, Wei ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Question about volume matrix in hippocampus
External Email - Use Caution Hi. Dear Eugenio Thanks for your reply, could you be more specific? I have tried many times with this command but with the same problem happened. For example, I use the one subject quantifyHAsubregions.sh hippoSf T1-AVP6176 At_risk/volume And the feedback Gathering results from subjects in: /home/weishao/At_risk Using the prefix name: hippoSf Using the suffix name: T1-AVP6176 And writing them to: home/weishao/At_risk/volume However, there is no result text file in the output directory. [weishao@gra-login1 ~]$ cd At_risk/volume/ [weishao@gra-login1 volume]$ ls -ltr total 0 The attachment is the original script of quantifyHAsubregions.sh Best, Wei On Thu, Apr 22, 2021 at 3:21 PM Iglesias Gonzalez, Juan E. < jiglesiasgonza...@mgh.harvard.edu> wrote: > Dear Wei, > > The syntax of the command is: > > quantifyHAsubregions.sh hippoSf - > > > > > > > > > Juan Eugenio Iglesias > > Senior research fellow > > CMIC (UCL), MGH (HMS) and CSAIL (MIT) > > http://secure-web.cisco.com/1JMQZFodc2ZeKRIdC2wNQ0ofo-HaHdAORal7oOrAUz7-tO2Db6jV2MPQlWKnNLpvTrElx5paBPy1YOLk30wxeHcCllCk3q5WOD4BnvbPHdgEhA6cvcruA5SVQ2qDFypia0sqAoSxitVKwVD5WPcVZbZ_1EaSdxIgIcxRhGawHn0jEe4JWpIl7gqXA1LRXVl43wYcE-ht-QPEKXwmx4MdvE5vE8Rkm_nXchVsr6tvSvnaW1Z8RtnHlfKKEFGQFHXemMfXSGkYwZucCJJ8aVMipyw/http%3A%2F%2Fwww.jeiglesias.com > > > > > > > > *From: * on behalf of Wei Shao < > ws...@research.baycrest.org> > *Reply-To: *Freesurfer support list > *Date: *Thursday, April 22, 2021 at 15:10 > *To: *Freesurfer support list > *Subject: *Re: [Freesurfer] Question about volume matrix in hippocampus > > > > *External Email - Use Caution* > > Hi, Eugenio > > > > Thanks for your kind reply. I have tried this command with a dataset and > it wasn't function. > > > > For example, Here is my script > > > > #!/bin/bash > > module load freesurfer/7.1.0 > source $EBROOTFREESURFER/FreeSurferEnv.sh > export SUBJECTS_DIR=/home/weishao/At_risk > > quantifyHAsubregions.sh hippoSf sub-AVP8580 sub-AVP6176 sub-BAY10224 > /home/weishao/At_risk > > *And there is the feedback * > > > > Gathering results from subjects in: >sub-BAY10224 > Using the prefix name: >hippoSf > Using the suffix name: >sub-AVP8580 > And writing them to: >sub-AVP6176 > /project/6019291/shared/software/2017/Core/freesurfer/7.1.0/bin/quantifyHAsubregions.sh: > line 8: cd: sub-BAY10224: No such file or directory > failed to do cd sub-BAY10224 > > > > I also tried this with one subject, > > > > And I don't find the text file at /home/weishao/At_risk, I also tried > this with one subject, couldn't find the text file neither. > > > > Would you mind tell me where I did wrong? Thanks > > > > Best, > > Wei > > > > On Wed, Apr 21, 2021 at 5:26 PM Iglesias Gonzalez, Juan E. < > jiglesiasgonza...@mgh.harvard.edu> wrote: > > Dear Wei, > > All the volume measurements use the underlying probabilities with the > maximum level of granularity. > > Kind regards, > > Eugenio > > > > > > 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* > http://secure-web.cisco.com/1JMQZFodc2ZeKRIdC2wNQ0ofo-HaHdAORal7oOrAUz7-tO2Db6jV2MPQlWKnNLpvTrElx5paBPy1YOLk30wxeHcCllCk3q5WOD4BnvbPHdgEhA6cvcruA5SVQ2qDFypia0sqAoSxitVKwVD5WPcVZbZ_1EaSdxIgIcxRhGawHn0jEe4JWpIl7gqXA1LRXVl43wYcE-ht-QPEKXwmx4MdvE5vE8Rkm_nXchVsr6tvSvnaW1Z8RtnHlfKKEFGQFHXemMfXSGkYwZucCJJ8aVMipyw/http%3A%2F%2Fwww.jeiglesias.com > <http://secure-web.cisco.com/1bK9Xmm7cNRBWH73XeUE3ROyYVFC0VU8bFAuK6d5WSElLPFE2zDlSEpKsgjrFb1ckAVriuarMf8sfizjd-Jxqz0Z_7NkO1ndGSwPXmMj7979KyP1iHCiaTdPkN869_aFAGbUN4ZLUsqbJjwIXhzhty2QQp4GqBy1FXa5ws4z6kQxH4k-DGASyP0cXn1OYAvtGNGD1ijRcivM59q-wKnNALtSFPWo50p9qmikNWzoeYfPt9n6qvFUzRNqe6IpfhpzgtArpyYdRc_Yiz0T6Kfy8xg/http%3A%2F%2Fwww.jeiglesias.com> > > > > > > > > > *From: * on behalf of Wei Shao < > ws...@research.baycrest.org> > *Reply-To: *Freesurfer support list > *Date: *Wednesday, April 21, 2021 at 17:20 > *To: *Freesurfer support list > *Subject: *[Freesurfer] Question about volume matrix in hippocampus > > > > *External Email - Use Caution* > > Hi, Freesurfer experts. > > > > I have used "quantifyHAsubregions.sh hippoSf" to gather the volume > information from the hippocampus
Re: [Freesurfer] Question about volume matrix in hippocampus
External Email - Use Caution
Hi, Eugenio
Thanks for your kind reply. I have tried this command with a dataset and it
wasn't function.
For example, Here is my script
#!/bin/bash
module load freesurfer/7.1.0
source $EBROOTFREESURFER/FreeSurferEnv.sh
export SUBJECTS_DIR=/home/weishao/At_risk
quantifyHAsubregions.sh hippoSf sub-AVP8580 sub-AVP6176 sub-BAY10224
/home/weishao/At_risk
*And there is the feedback *
Gathering results from subjects in:
sub-BAY10224
Using the prefix name:
hippoSf
Using the suffix name:
sub-AVP8580
And writing them to:
sub-AVP6176
/project/6019291/shared/software/2017/Core/freesurfer/7.1.0/bin/quantifyHAsubregions.sh:
line 8: cd: sub-BAY10224: No such file or directory
failed to do cd sub-BAY10224
I also tried this with one subject,
And I don't find the text file at /home/weishao/At_risk, I also tried this
with one subject, couldn't find the text file neither.
Would you mind tell me where I did wrong? Thanks
Best,
Wei
On Wed, Apr 21, 2021 at 5:26 PM Iglesias Gonzalez, Juan E. <
jiglesiasgonza...@mgh.harvard.edu> wrote:
> Dear Wei,
>
> All the volume measurements use the underlying probabilities with the
> maximum level of granularity.
>
> Kind regards,
>
> Eugenio
>
>
>
>
>
> Juan Eugenio Iglesias
>
> Senior research fellow
>
> CMIC (UCL), MGH (HMS) and CSAIL (MIT)
>
> http://secure-web.cisco.com/1bK9Xmm7cNRBWH73XeUE3ROyYVFC0VU8bFAuK6d5WSElLPFE2zDlSEpKsgjrFb1ckAVriuarMf8sfizjd-Jxqz0Z_7NkO1ndGSwPXmMj7979KyP1iHCiaTdPkN869_aFAGbUN4ZLUsqbJjwIXhzhty2QQp4GqBy1FXa5ws4z6kQxH4k-DGASyP0cXn1OYAvtGNGD1ijRcivM59q-wKnNALtSFPWo50p9qmikNWzoeYfPt9n6qvFUzRNqe6IpfhpzgtArpyYdRc_Yiz0T6Kfy8xg/http%3A%2F%2Fwww.jeiglesias.com
>
>
>
>
>
>
>
> *From: * on behalf of Wei Shao <
> ws...@research.baycrest.org>
> *Reply-To: *Freesurfer support list
> *Date: *Wednesday, April 21, 2021 at 17:20
> *To: *Freesurfer support list
> *Subject: *[Freesurfer] Question about volume matrix in hippocampus
>
>
>
> *External Email - Use Caution*
>
> Hi, Freesurfer experts.
>
>
>
> I have used "quantifyHAsubregions.sh hippoSf" to gather the volume
> information from the hippocampus. A quick question about the volume matrix,
> would you tell me which label system ("HBT" "FS60" or "CA") this code used
> to extract the volume information? or there is no difference? Thanks
>
>
>
> Best,
>
> Wei
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://secure-web.cisco.com/1bQET30Fd0RkuxVIyhifmZHJ3AlO4xEABPW1K8Bvre1kGrSRcUyKdtKjdls2IuomAJH0iNCJZ2_eQwvRWJBzBISplYRjFd8HjHoAyNs8Ys1RK0M-B4P_fa61AnpXcle-ywuhZxB6m4xq1_XMhXnf65iT64b52KGVVV1UGlRkboRnfbkLrioI1B1xrIJATAumn0KJMKkw8dcfoLQarDrUMAkrLVmy3Va0sEEJnpkCXKiuKtFD9aYTWil-Y5JAumMa52gBiPnyzqpRS_g-8-ujtWQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
> The information in this e-mail is intended only for the person to whom it
> is addressed. If you believe this e-mail was sent to you in error and the
> e-mail contains patient information, please contact the Mass General
> Brigham Compliance HelpLine at
> http://secure-web.cisco.com/1gzeDXQNgVL-J-dSTU8cX3uw7PjDlmyFpQuy24BIEEjmKnkexbBn8i1UW-3eSV0ulGKBuFTb1G5iPnvbKZkEcJKg6YMJaI4WA5kD9gFJOQ3r_p3htvczAHvsr92wM3DORhzOPCZw8BoZ_CEue1UYWa_WYwVczPaw6hlTFPVar2jWNOkvog_P8xDbq-6WsGONKqRnyOoXa4hz37MRJqfKYR8AMglppnARk30DSC8o4-RRPkld24v9ZVYI1kd8MK441KFkEDeG6c92CwB6oGgIQaA/http%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline
> . If the e-mail was sent
> to you in error but does not contain patient information, please contact
> the sender and properly dispose of the e-mail.
> Please note that this e-mail is not secure (encrypted). If you do not
> wish to continue communication over unencrypted e-mail, please notify the
> sender of this message immediately. Continuing to send or respond to
> e-mail after receiving this message means you understand and accept this
> risk and wish to continue to communicate over unencrypted e-mail.
>
___
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https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Question about volume matrix in hippocampus
External Email - Use Caution
Hi, Freesurfer experts.
I have used "quantifyHAsubregions.sh hippoSf" to gather the volume
information from the hippocampus. A quick question about the volume matrix,
would you tell me which label system ("HBT" "FS60" or "CA") this code used
to extract the volume information? or there is no difference? Thanks
Best,
Wei
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Freesurfer/6.0.0 license
External Email - Use Caution Hello, Freesurfer experts I have used Freesurfer/6.0.0 in order to run FastSurfer https://secure-web.cisco.com/12C5JQprff2Y8YL4t7AWGn9XhCzBPeQ7qRNQPcetjS7kldVEPElI-HBY4lvBwmcGWPng5XPsW7emsFxfyef1JeRdMP7sMkqWm7IEO8tzrW7UTSYMJ2MDjJp2w0ehQ5L6Q9P17wvylT89WxIKeMCuTG7ndT3RxP_jRXk3OAv6k6O6D9RBTWOLzwuG1y0KsdVkt8CzkthsjFeGjk0_5IlubjtGznNBOu28M6FPwj5vM4wVgQLK3ySliEXORgtU0qduGLINjgj7iMOr5iIZ_UYLA-A/https%3A%2F%2Fgithub.com%2FDeep-MI%2FFastSurfe. And copy the latest license.txt into the Freesurfer/6.0.0 home directory. Here is the problem every time I run FastSurfer, The attachment is the full log GNU libc version: 2.17 ERROR: Systems running GNU glibc version greater than 2.15 require a newly formatted license file (it's free). Please download a new one from the following page: http://secure-web.cisco.com/1K8wEaOjxHfI-SY43wEEp8bk2OLIpUlwQ6KolO1v5nULkvtq_K7eZ-3gSs__1C9lpsxqWwwuRd02IvR0cY5m-wN5Y1_dzXHJ1omDX27wOuKpaBiusuVYnvOG1DhMC_YvtSaLVKO3OsN_8l7RuV56Kg5IKuHEZxXES_0NLgJ1MY8NvLeeX75ZEgXBWGixgRBKkuwO3iIbAckCU2HLFdIBj_iN-v9yB0QcC6WAi3g__WBftAwNzt-iaywPtiWdXpSaooUjQqycGmnnmvq5zdUdFZg/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fregistration.html Could you give me some suggestions? Thanks Best, We slurm-45540976.out Description: Binary data ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Hippocampal subfield segmentation
External Email - Use Caution Hi, Dr. Iglesias Gonzalez Here is the full log, Thanks Best, Wei On Mon, Mar 1, 2021 at 10:33 PM Iglesias Gonzalez, Juan E. < jiglesiasgonza...@mgh.harvard.edu> wrote: > Dear Wei, > > Can you please provide us with the full log? > > Cheers, > > /E > > > > > > Juan Eugenio Iglesias > > Senior research fellow > > CMIC (UCL), MGH (HMS) and CSAIL (MIT) > > http://secure-web.cisco.com/1QG7uGIHTOdZ2Mb_tpU68iZ_owRYsTQl1DBCO6QrSAb64Kb0Rzx4ZOx3LNeUg8cYWEvLm-ybTeV1JGTHuVgY1mPHQkB2CmTV1abh94ZqQMIdEuu9BWHGad2nW93ap3bPSQo7vfA2A8K_RNQcgq4iyn6EPQbMinxBF5sIhnLQ8afvzuSH1H7FKJPfFaASueXmm0wAWzLcQfenpnINPHN0pxmolEUVEIxDvF6S9Sy1lCrwLo2vFrA_dVs0tjaG_TwJXCb4SCij-8ijuqTNnJ26T-A/http%3A%2F%2Fwww.jeiglesias.com > > > > > > > > *From: * on behalf of Wei Shao < > ws...@research.baycrest.org> > *Reply-To: *Freesurfer support list > *Date: *Monday, March 1, 2021 at 21:14 > *To: *Freesurfer support list > *Subject: *[Freesurfer] Hippocampal subfield segmentation > > > > *External Email - Use Caution* > > Hi, Freesurfer expert > > > > I tried Hippocampal subfield segmentation with an additional T2 scan by > using FS7.1.0 > > > > Here is the log error massage > > > > Attempted to access cropping(1); index out of bounds because > numel(cropping)=0. > > Error in applyCropping (line 7) > > > > Error in segmentSubjectT1T2_autoEstimateAlveusML (line 950) > > > > MATLAB:badsubscript > @#@FSTIME 2021:03:01:20:38:39 > run_segmentSubjectT1T2_autoEstimateAlveusML.sh N 18 e 243.67 S 3.47 U > 220.01 P 91% M 1248336 F 144 R 909119 W 0 c 49601 w 14948 I 320352 O 429920 > L 30.66 34.91 35.10 > @#@FSLOADPOST 2021:03:01:20:42:43 > run_segmentSubjectT1T2_autoEstimateAlveusML.sh N 18 47.20 43.27 38.55 > Linux gra813 3.10.0-1127.8.2.el7.x86_64 #1 SMP Tue May 12 16:57:42 UTC > 2020 x86_64 GNU/Linux > > T2 hippocampal subfields exited with ERRORS at Mon Mar 1 20:42:43 EST 2021 > > For more details, see the log file > /home/weishao//BAY11958/scripts/hippocampal-subfields-T2.T2.log > > > > Could you tell me how to fix this? Thanks. > > > > > > Best, > > Wei > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://secure-web.cisco.com/1yoXS6dKZ-NgQmNn6ZWsu7E6Fy28mmAvwujVOWjd0TXC-2rnYtbfOToNdj8FNRMl9_r5G8pvA0y52cLEZFh6ArDsWdkuOwbOa_KluGStvj2OQyVepzLH4HE5ODIpzKRsK15XP970jorSINqsZRyBgnFcxFZJRes9cFrFSURI2jqckcNTD2AWH86HiraJqydQcHdqq2GxQ-BMsVtdOi98xqbXk3kJAxAf1hR-bNclwgewkP4DdSlUYTpBkzn5HP-hCNXbNCr3uIvKMC0MLJz68nQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer slurm-45279731.out Description: Binary data ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Hippocampal subfield segmentation
External Email - Use Caution Hi, Freesurfer expert I tried Hippocampal subfield segmentation with an additional T2 scan by using FS7.1.0 Here is the log error massage Attempted to access cropping(1); index out of bounds because numel(cropping)=0. Error in applyCropping (line 7) Error in segmentSubjectT1T2_autoEstimateAlveusML (line 950) MATLAB:badsubscript @#@FSTIME 2021:03:01:20:38:39 run_segmentSubjectT1T2_autoEstimateAlveusML.sh N 18 e 243.67 S 3.47 U 220.01 P 91% M 1248336 F 144 R 909119 W 0 c 49601 w 14948 I 320352 O 429920 L 30.66 34.91 35.10 @#@FSLOADPOST 2021:03:01:20:42:43 run_segmentSubjectT1T2_autoEstimateAlveusML.sh N 18 47.20 43.27 38.55 Linux gra813 3.10.0-1127.8.2.el7.x86_64 #1 SMP Tue May 12 16:57:42 UTC 2020 x86_64 GNU/Linux T2 hippocampal subfields exited with ERRORS at Mon Mar 1 20:42:43 EST 2021 For more details, see the log file /home/weishao//BAY11958/scripts/hippocampal-subfields-T2.T2.log Could you tell me how to fix this? Thanks. Best, Wei ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Hippocampal subfield segmentation by T2 scan
External Email - Use Caution Hi, dear Freesurfer team I used sagittal T1(MPRAGE-sag_T1w.nii.gz) to recon-all and did the hippo-subfield segmentation on T1, but when I tried to use the additional scan by segmentHA_T2.sh : segmentHA_T2.sh sub-AVP14352 /home/weishao/sub-AVP14352/Ses-01/anat/sub-AVP14352_ses-01_cor_run-01_T2w.nii.gz sub-AVP14352_T2 0 Here is the feedback Error using kvlGEMSMatlab std::bad_alloc Error in kvlReadCroppedImage (line 11) Error in segmentSubjectT2_autoEstimateAlveusML (line 930) @#@FSTIME 2021:02:19:13:38:45 run_segmentSubjectT2_autoEstimateAlveusML.sh N 18 e 385.18 S 24.62 U 646.85 P 174% M 1033292 F 130 R 2612883 W 0 c 193519 w 290275 I 2443704 O 429952 L 3.35 3.58 5.40 @#@FSLOADPOST 2021:02:19:13:45:10 run_segmentSubjectT2_autoEstimateAlveusML.sh N 18 5.71 5.26 5.58 Linux gra-login1 3.10.0-1127.8.2.el7.x86_64 #1 SMP Tue May 12 16:57:42 UTC 2020 x86_64 GNU/Linux T2 hippocampal subfields exited with ERRORS at Fri Feb 19 13:45:11 EST 2021 Could you tell me what I should do to fix this? Thanks Best, Wei ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Multiple subjects with segmentHA_T1.sh
External Email - Use Caution Hi, Dear Freesurfer team I'm wondering is there any command/information that can help to run multiple subjects with segmentHA_T1.sh at one time? Thanks Best, Wei ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Parallel computing for recon-all
External Email - Use Caution Hi, Freesufer experts Sorry for the late reply, I have tried again with openmp 8 flag and added the cpus-per-task=16 for a subject. I have cut the recon-all processing time from 06:17:14 to 03:32:21! So excited. By the way, Could you help me to understand this command? export OMP_NUM_THREADS=$SLURM_CPUS_PER_TASK From what I understand, if I apply this code for recon-all, this command assigns the total threads of recon-all task = number of the cpu used in the recon-all task? I know a cpu can handle multiples threads, is this mean that only one thread to one cpu for the recon-all task? Best, Wei On Fri, Jan 29, 2021 at 10:53 AM Douglas N. Greve wrote: > No, all the results are fine. By "broken" I mean that it might crash in > places that it would not have crashed in v6 or that it just would not > have been running in parallel when you think it was. > > On 1/28/2021 3:48 PM, Michael Krause wrote: > > External Email - Use Caution > > > > On 1/28/21 6:00 PM, Douglas N. Greve wrote: > >> No, use of -threads or -openmp will always trigger the openmp code. The > >> -parallel may introduce other parallel. I did not write this part of the > >> code so I'm not sure, and I think I might have broken the -parallel > >> implementation when I did the last recon-all rewrite > > Ah, that's good to know. I will remove the redundancy in our scripts > then. > > > > What do you mean by "may have broken"? Broken as in we have to worry > about > > results? We are currently running a couple of thousand subjects with > 7.1.1 > > and they appear to be running fine so far *with* -parallel and -openmp 4 > > with an average core utilization of around 2.4 out of the possible 4. > > > > cheers > > Michael Krause > > > > ___ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://secure-web.cisco.com/1x1FDZItu_iknOi5S4MQ7eWCXCrNKoHyIpbIzQsfN4GnSDCjOyXy3kp8OfLt-7YyV7WgFwH2QpOtwJt1SZ6vVVUWqbIfTAHGEyxJSpkXF-mNroJRELpRhpqgQDCDweSaiQkKLfBBGKf33Q9KFyzLzJc_1DLl3wdcGXR0CDJ882WuvH1YyrZdsHjWX_-69ehG3CMWgIX3hM04i_TR4dgU_Pp2zEZIbjVphSRB3QORhMrmnlC97s7_FjaoyxdZVturIgMFwdGpKnNp2L93i64F8aA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://secure-web.cisco.com/1x1FDZItu_iknOi5S4MQ7eWCXCrNKoHyIpbIzQsfN4GnSDCjOyXy3kp8OfLt-7YyV7WgFwH2QpOtwJt1SZ6vVVUWqbIfTAHGEyxJSpkXF-mNroJRELpRhpqgQDCDweSaiQkKLfBBGKf33Q9KFyzLzJc_1DLl3wdcGXR0CDJ882WuvH1YyrZdsHjWX_-69ehG3CMWgIX3hM04i_TR4dgU_Pp2zEZIbjVphSRB3QORhMrmnlC97s7_FjaoyxdZVturIgMFwdGpKnNp2L93i64F8aA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Parallel computing for recon-all
External Email - Use Caution Hi, Douglas Thanks for your kind reply. 1 I run the same subject on a server with openmp 8 flags cost 7 hours, without openmp 8 flag would be 7h10minutes. 3 Could you be more specific about run them by hand? is this mean I run different tasks like skull strip or parcellation separately within recon rather than recon-all? Best, Wei On Mon, Jan 25, 2021 at 10:17 PM Douglas N. Greve wrote: > > > On 1/20/2021 3:39 PM, Wei Shao wrote: > > External Email - Use Caution > Hi, Freesufer experts > > My name is wei shao, I have a few questions regarding the > parallel computing of recon-all > > 1 According to documents, freesurfer is OpenMP code , I use -openmp 8 flag > like: recon-all -alli -i input.file -s output.file -openmp 8 > to tun the recon command on a server, but it doesn't work for me (the > running time is very similar for the same subject). Cloud you tell me > what is wrong? > > Please specify the difference in times. > > > 2 Can Freesufer take advantage of several GPUs? > > No > > > 3 Is it possible to open few threads to run recon-all on different > sections parallelly? > > Only if you run them by hand > > > Best, > Wei > > > > ___ > Freesurfer mailing > listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://secure-web.cisco.com/1iCbpbp3TlQC67E9mq0PzTzJ5cANh6TRxDqcmmQi1W7zG1jM5MCUQqqsXe3QwM7oVOFj_LjCFo27-8CJfoyO91GKrSBzIxnU_YshInte2aLVCn47Vj32-jMMVrD8rT-_76qE6PP6khCI7B6FR2Yp5MsZI8wpfQDHkafQjCjJcDl8xcasuz_GtojXgPZ9v09wpG8dwOWxahtMB8ldo_6U1rwqRG3OFUZCwWs26DrqqA8xjv-XgB_FKSSrhHHo8xSgDo6iwlh8PgiT7FQY9ZGz_TQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Parallel computing for recon-all
External Email - Use Caution Hi, Freesufer experts My name is wei shao, I have a few questions regarding the parallel computing of recon-all 1 According to documents, freesurfer is OpenMP code , I use -openmp 8 flag like: recon-all -alli -i input.file -s output.file -openmp 8 to tun the recon command on a server, but it doesn't work for me (the running time is very similar for the same subject). Cloud you tell me what is wrong? 2 Can Freesufer take advantage of several GPUs? 3 Is it possible to open few threads to run recon-all on different sections parallelly? Best, Wei ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Talairach Failure in recon-subject {Disarmed}
External Email - Use Caution Hi, Freesurfer team I have met a Talairach Failure problem when running the recon -all for a subject, here is the feedback: I tried -notal-check flag, but it might cause another problem when I use segmentHA_T2.sh to do hippocampus subfield segmentation. So, Could you help me to solve this problem? Thanks. # #@# Talairach Failure Detection Mon Dec 21 17:59:09 EST 2020 /scratch/weishao/20191017_BAY10224/sub-BAY10224_Negar/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0., pval=0. < threshold=0.0050) @#@FSTIME 2020:12:21:17:59:09 talairach_afd N 4 e 0.07 S 0.01 U 0.00 P 18% M 6672 F 0 R 2777 W 0 c 2 w 65 I 1504 O 0 L 12.75 18.35 27.51 @#@FSLOADPOST 2020:12:21:17:59:09 talairach_afd N 4 12.75 18.35 27.51 Manual Talairach alignment may be necessary, or include the -notal-check flag to skip this test, making sure the -notal-check flag follows -all or -autorecon1 in the command string. See: http://secure-web.cisco.com/1_6NU0uyplJn2Ny1P23HKLCy4v6xjIjGaWl1oZJY8FTyZ1fbUcZRmKspBxJlynhFmyDvpB5zZydgw7W3SM9hfCGvOLgESAsRsl5GyKDdulFu6aduP94X2BwjqSgZuvL3d7rTq_jfDF4gvVTlEB-H2_0of1E2u0x2DmzaMGFxXXlThHkPTCEUhRUm2Q3TfaGcYJ0vrvkyH1DlUbexb5LjdlaCyvOG8taQiQJdq2aAzbUFSkkOwqCCSRS4JeXLEiyjtfs-wjC9QWC_BlhloyUfmbw/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FTalairach ERROR: Talairach failed! Linux gra824 3.10.0-1127.8.2.el7.x86_64 #1 SMP Tue May 12 16:57:42 UTC 2020 x86_64 GNU/Linux recon-all -s sub-BAY10224_Negar exited with ERRORS at Mon Dec 21 17:59:09 EST 2020 Best, Wei : ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] convert to native space
External Email - Use Caution Hello, Freesurfer team This is Wei Shao, I was trying to convert the freesurfer automatic segmentation of the hippocampus subfield into native space so I can compare it with the manual segmentation. Here is the command: mri_label2vol --seg lh.hippoAmygLabels-BAYX-T2.v21.CA.mgz --temp rawavg.mgz --o lh.hippo-BAYX.mgz --regheader aseg.mgz 1 Could you tell me which files I should use in terms of the temp and regheader flag. 2 the manual segmentation based on T2 image, do I need to use the same T2 image as the overlaid image when it comes to Freeview? I think the nu.mgz is T1 image, could you tell me where I can find the T2 image accordingly? 3 do you know any command that can help me to check the information of the .mgz file like the 3dinfo command? I really appreciate your help, Thanks. Best, Wei ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] eddy_correct with DTI {Disarmed}
External Email - Use Caution Hi, Douglas Sorry to bother you again, do you think the problem is the old version of FSL? Best, Wei On Fri, Nov 13, 2020 at 1:32 PM Wei Shao wrote: > Hi Douglas > > I think it's 5.0.11 > > [weishao@gra-login2 ~]$ module load nixpkgs/16.09 freesurfer/7.1.0 > To initialize FreeSurfer, > do (sh, ash, ksh, and bash) > source $EBROOTFREESURFER/FreeSurferEnv.sh > or (csh, tcsh) > $EBROOTFREESURFER/FreeSurferEnv.csh > > [weishao@gra-login2 ~]$ module load fsl > [weishao@gra-login2 ~]$ which fsl > /cvmfs/ > soft.computecanada.ca/easybuild/software/2017/avx2/Compiler/intel2016.4/fsl/5.0.11/fsl/bin/fsl > [weishao@gra-login2 ~]$ > > Best, > Wei > > On Fri, Nov 13, 2020 at 10:11 AM Douglas N. Greve > wrote: > >> What version of FSL are you using? >> >> On 11/10/2020 12:19 AM, Wei Shao wrote: >> >> External Email - Use Caution >> Hi, Freesurfer team, >> >> My name is Weishao, Here is a problem that bothers me a lot I try to run >> DTI. I have loaded the FSL module and use the most recent version of >> Freesurfer. it's appreciated if someone can help. Thanks. >> >> Here is the script. >> >> dt_recon --b sub-AVP6176_ses-01_dir-sfs_run-01_dwi.bval >> sub-AVP6176_ses-01_dir-sfs_run-01_dwi.bvec >> --i sub-AVP6176_ses-01_dir-sfs_run-01_dwi.nii.gz >> --s /home/weishao/scratch/rawdata/sub-AVP6176/ >> --o /home/weishao/scratch/rawdata/sub-AVP6176/ >> >> Here is feedback >> >> -rw-r- 1 weishao weishao 49041968 Sep 9 11:41 >> /scratch/weishao/rawdata/sub-AVP6176/Ses-01/dwi/sub-AVP6176_ses-01_dir-sfs_run-01_dwi.nii.gz >> INFO: SUBJECTS_DIR is >> /project/6019291/shared/software/2017/Core/freesurfer/7.1.0/subjects >> dt_recon logfile >> Tue Oct 27 16:19:28 EDT 2020 >> VERSION dt_recon 7.1.0 >> setenv SUBJECTS_DIR >> /project/6019291/shared/software/2017/Core/freesurfer/7.1.0/subjects >> cd /scratch/weishao/rawdata/sub-AVP6176/Ses-01/dwi >> /project/6019291/shared/software/2017/Core/freesurfer/7.1.0/bin/dt_recon >> --b sub-AVP6176_ses-01_dir-sfs_run-01_dwi.bval >> sub-AVP6176_ses-01_dir-sfs_run-01_dwi.bvec --i >> sub-AVP6176_ses-01_dir-sfs_run-01_dwi.nii.gz --s >> /home/weishao/scratch/rawdata/sub-AVP6176/ --o >> /home/weishao/scratch/rawdata/sub-AVP6176/ >> gra95 >> weishao >> /cvmfs/*MailScanner has detected a possible fraud attempt from >> "secure-web.cisco.com" claiming to be* >> soft.computecanada.ca/easybuild/software/2017/avx2/Compiler/intel2016.4/fsl/5.0.11/fsl/bin/eddy_correct >> <http://secure-web.cisco.com/13U2x8LxxvC3rroBw84sAsKDdxMd5ljIVys9mm4GHsZ9POUe_Tuj6j5w-u-GyyTjqBYGzFd1dY9MHjviD0OXpTo6uQ5RGuWfFs2oG7LMgx4I0t3T32dv4FD07YfnDPzCDutwQfTp2Ui_MDmBfX9AyaMsSONb-9atBJd4cLo2d2fHV4K6QVDfxwYUjBMvYozC1_VxhPa3XI-Yzkt8JU2cwsw/http%3A%2F%2Fsoft.computecanada.ca%2Feasybuild%2Fsoftware%2F2017%2Favx2%2FCompiler%2Fintel2016.4%2Ffsl%2F5.0.11%2Ffsl%2Fbin%2Feddy_correct> >> ECRefTP 0 >> #@#--- >> Converting input >> Tue Oct 27 16:19:28 EDT 2020 >> cd /scratch/weishao/rawdata/sub-AVP6176/Ses-01/dwi >> mri_convert >> /scratch/weishao/rawdata/sub-AVP6176/Ses-01/dwi/sub-AVP6176_ses-01_dir-sfs_run-01_dwi.nii.gz >> /scratch/weishao/rawdata/sub-AVP6176/dwi.nii.gz >> mri_convert >> /scratch/weishao/rawdata/sub-AVP6176/Ses-01/dwi/sub-AVP6176_ses-01_dir-sfs_run-01_dwi.nii.gz >> /scratch/weishao/rawdata/sub-AVP6176/dwi.nii.gz >> reading from >> /scratch/weishao/rawdata/sub-AVP6176/Ses-01/dwi/sub-AVP6176_ses-01_dir-sfs_run-01_dwi.nii.gz... >> TR=4000.00, TE=0.00, TI=0.00, flip angle=0.00 >> i_ras = (-0.999608, 0.017447, -0.021891) >> j_ras = (0.0104682, 0.958258, 0.285714) >> k_ras = (-0.0259621, -0.285373, 0.958065) >> writing to /scratch/weishao/rawdata/sub-AVP6176/dwi.nii.gz... >> >> >> #@#--- >> Eddy/Motion Correct >> Tue Oct 27 16:19:44 EDT 2020 >> cd /scratch/weishao/rawdata/sub-AVP6176/ectmp >> eddy_correct /scratch/weishao/rawdata/sub-AVP6176/dwi.nii.gz >> /scratch/weishao/rawdata/sub-AVP6176/dwi-ec.nii.gz 0 >> /cvmfs/*MailScanner has detected a possible fraud attempt from >> "secure-web.cisco.com" claiming to be* >> soft.computecanada.ca/easybuild/software/2017/avx2/Compiler/intel2016.4/fsl/5.0.11/fsl/bin/eddy_correct >> <http://secure-web.cisco.com/13U2x8LxxvC3rroBw84sAsKDdxMd5ljIVys9mm4GHsZ9POUe_Tuj6j5w-u-GyyTjqBYGzFd1dY9MHjviD0OXpTo6uQ5RGuWfFs2oG7LMgx4I0t3T32dv4FD07YfnDPzCDutwQfTp2Ui_MDmBfX9AyaMsSONb-9atBJd4cLo2d2fHV4K6QVDfxwYUjBMvYozC1
Re: [Freesurfer] eddy_correct with DTI {Disarmed}
External Email - Use Caution Hi Douglas I think it's 5.0.11 [weishao@gra-login2 ~]$ module load nixpkgs/16.09 freesurfer/7.1.0 To initialize FreeSurfer, do (sh, ash, ksh, and bash) source $EBROOTFREESURFER/FreeSurferEnv.sh or (csh, tcsh) $EBROOTFREESURFER/FreeSurferEnv.csh [weishao@gra-login2 ~]$ module load fsl [weishao@gra-login2 ~]$ which fsl /cvmfs/ soft.computecanada.ca/easybuild/software/2017/avx2/Compiler/intel2016.4/fsl/5.0.11/fsl/bin/fsl [weishao@gra-login2 ~]$ Best, Wei On Fri, Nov 13, 2020 at 10:11 AM Douglas N. Greve wrote: > What version of FSL are you using? > > On 11/10/2020 12:19 AM, Wei Shao wrote: > > External Email - Use Caution > Hi, Freesurfer team, > > My name is Weishao, Here is a problem that bothers me a lot I try to run > DTI. I have loaded the FSL module and use the most recent version of > Freesurfer. it's appreciated if someone can help. Thanks. > > Here is the script. > > dt_recon --b sub-AVP6176_ses-01_dir-sfs_run-01_dwi.bval > sub-AVP6176_ses-01_dir-sfs_run-01_dwi.bvec > --i sub-AVP6176_ses-01_dir-sfs_run-01_dwi.nii.gz > --s /home/weishao/scratch/rawdata/sub-AVP6176/ > --o /home/weishao/scratch/rawdata/sub-AVP6176/ > > Here is feedback > > -rw-r- 1 weishao weishao 49041968 Sep 9 11:41 > /scratch/weishao/rawdata/sub-AVP6176/Ses-01/dwi/sub-AVP6176_ses-01_dir-sfs_run-01_dwi.nii.gz > INFO: SUBJECTS_DIR is > /project/6019291/shared/software/2017/Core/freesurfer/7.1.0/subjects > dt_recon logfile > Tue Oct 27 16:19:28 EDT 2020 > VERSION dt_recon 7.1.0 > setenv SUBJECTS_DIR > /project/6019291/shared/software/2017/Core/freesurfer/7.1.0/subjects > cd /scratch/weishao/rawdata/sub-AVP6176/Ses-01/dwi > /project/6019291/shared/software/2017/Core/freesurfer/7.1.0/bin/dt_recon > --b sub-AVP6176_ses-01_dir-sfs_run-01_dwi.bval > sub-AVP6176_ses-01_dir-sfs_run-01_dwi.bvec --i > sub-AVP6176_ses-01_dir-sfs_run-01_dwi.nii.gz --s > /home/weishao/scratch/rawdata/sub-AVP6176/ --o > /home/weishao/scratch/rawdata/sub-AVP6176/ > gra95 > weishao > /cvmfs/*MailScanner has detected a possible fraud attempt from > "secure-web.cisco.com" claiming to be* > soft.computecanada.ca/easybuild/software/2017/avx2/Compiler/intel2016.4/fsl/5.0.11/fsl/bin/eddy_correct > <http://secure-web.cisco.com/13U2x8LxxvC3rroBw84sAsKDdxMd5ljIVys9mm4GHsZ9POUe_Tuj6j5w-u-GyyTjqBYGzFd1dY9MHjviD0OXpTo6uQ5RGuWfFs2oG7LMgx4I0t3T32dv4FD07YfnDPzCDutwQfTp2Ui_MDmBfX9AyaMsSONb-9atBJd4cLo2d2fHV4K6QVDfxwYUjBMvYozC1_VxhPa3XI-Yzkt8JU2cwsw/http%3A%2F%2Fsoft.computecanada.ca%2Feasybuild%2Fsoftware%2F2017%2Favx2%2FCompiler%2Fintel2016.4%2Ffsl%2F5.0.11%2Ffsl%2Fbin%2Feddy_correct> > ECRefTP 0 > #@#--- > Converting input > Tue Oct 27 16:19:28 EDT 2020 > cd /scratch/weishao/rawdata/sub-AVP6176/Ses-01/dwi > mri_convert > /scratch/weishao/rawdata/sub-AVP6176/Ses-01/dwi/sub-AVP6176_ses-01_dir-sfs_run-01_dwi.nii.gz > /scratch/weishao/rawdata/sub-AVP6176/dwi.nii.gz > mri_convert > /scratch/weishao/rawdata/sub-AVP6176/Ses-01/dwi/sub-AVP6176_ses-01_dir-sfs_run-01_dwi.nii.gz > /scratch/weishao/rawdata/sub-AVP6176/dwi.nii.gz > reading from > /scratch/weishao/rawdata/sub-AVP6176/Ses-01/dwi/sub-AVP6176_ses-01_dir-sfs_run-01_dwi.nii.gz... > TR=4000.00, TE=0.00, TI=0.00, flip angle=0.00 > i_ras = (-0.999608, 0.017447, -0.021891) > j_ras = (0.0104682, 0.958258, 0.285714) > k_ras = (-0.0259621, -0.285373, 0.958065) > writing to /scratch/weishao/rawdata/sub-AVP6176/dwi.nii.gz... > > > #@#--- > Eddy/Motion Correct > Tue Oct 27 16:19:44 EDT 2020 > cd /scratch/weishao/rawdata/sub-AVP6176/ectmp > eddy_correct /scratch/weishao/rawdata/sub-AVP6176/dwi.nii.gz > /scratch/weishao/rawdata/sub-AVP6176/dwi-ec.nii.gz 0 > /cvmfs/*MailScanner has detected a possible fraud attempt from > "secure-web.cisco.com" claiming to be* > soft.computecanada.ca/easybuild/software/2017/avx2/Compiler/intel2016.4/fsl/5.0.11/fsl/bin/eddy_correct > <http://secure-web.cisco.com/13U2x8LxxvC3rroBw84sAsKDdxMd5ljIVys9mm4GHsZ9POUe_Tuj6j5w-u-GyyTjqBYGzFd1dY9MHjviD0OXpTo6uQ5RGuWfFs2oG7LMgx4I0t3T32dv4FD07YfnDPzCDutwQfTp2Ui_MDmBfX9AyaMsSONb-9atBJd4cLo2d2fHV4K6QVDfxwYUjBMvYozC1_VxhPa3XI-Yzkt8JU2cwsw/http%3A%2F%2Fsoft.computecanada.ca%2Feasybuild%2Fsoftware%2F2017%2Favx2%2FCompiler%2Fintel2016.4%2Ffsl%2F5.0.11%2Ffsl%2Fbin%2Feddy_correct>: > line 95: /cvmfs/*MailScanner has detected a possible fraud attempt from > "secure-web.cisco.com" claiming to be* > soft.computecanada.ca/easybuild/software/2017/avx2/Compiler/intel2016.4/fsl/5.0.11/fsl/bin/imglob > <http://secure-web.cisco.com/14GGFn_nc9xX-9O7KFUQlMhTcuKP2UzYHSyRZ1KY8WmZVDHlU9CvRqNtyi2-o9brT81R93N0ywcGuNRVh631lH6E_b01B9YCYcb1m95SVUKoP7sHDhles5fDfP-RqeSO5lJL1PRxEKZh
[Freesurfer] eddy_correct with DTI {Disarmed}
External Email - Use Caution Hi, Freesurfer team, My name is Weishao, Here is a problem that bothers me a lot I try to run DTI. I have loaded the FSL module and use the most recent version of Freesurfer. it's appreciated if someone can help. Thanks. Here is the script. dt_recon --b sub-AVP6176_ses-01_dir-sfs_run-01_dwi.bval sub-AVP6176_ses-01_dir-sfs_run-01_dwi.bvec --i sub-AVP6176_ses-01_dir-sfs_run-01_dwi.nii.gz --s /home/weishao/scratch/rawdata/sub-AVP6176/ --o /home/weishao/scratch/rawdata/sub-AVP6176/ Here is feedback -rw-r- 1 weishao weishao 49041968 Sep 9 11:41 /scratch/weishao/rawdata/sub-AVP6176/Ses-01/dwi/sub-AVP6176_ses-01_dir-sfs_run-01_dwi.nii.gz INFO: SUBJECTS_DIR is /project/6019291/shared/software/2017/Core/freesurfer/7.1.0/subjects dt_recon logfile Tue Oct 27 16:19:28 EDT 2020 VERSION dt_recon 7.1.0 setenv SUBJECTS_DIR /project/6019291/shared/software/2017/Core/freesurfer/7.1.0/subjects cd /scratch/weishao/rawdata/sub-AVP6176/Ses-01/dwi /project/6019291/shared/software/2017/Core/freesurfer/7.1.0/bin/dt_recon --b sub-AVP6176_ses-01_dir-sfs_run-01_dwi.bval sub-AVP6176_ses-01_dir-sfs_run-01_dwi.bvec --i sub-AVP6176_ses-01_dir-sfs_run-01_dwi.nii.gz --s /home/weishao/scratch/rawdata/sub-AVP6176/ --o /home/weishao/scratch/rawdata/sub-AVP6176/ gra95 weishao /cvmfs/ soft.computecanada.ca/easybuild/software/2017/avx2/Compiler/intel2016.4/fsl/5.0.11/fsl/bin/eddy_correct ECRefTP 0 #@#--- Converting input Tue Oct 27 16:19:28 EDT 2020 cd /scratch/weishao/rawdata/sub-AVP6176/Ses-01/dwi mri_convert /scratch/weishao/rawdata/sub-AVP6176/Ses-01/dwi/sub-AVP6176_ses-01_dir-sfs_run-01_dwi.nii.gz /scratch/weishao/rawdata/sub-AVP6176/dwi.nii.gz mri_convert /scratch/weishao/rawdata/sub-AVP6176/Ses-01/dwi/sub-AVP6176_ses-01_dir-sfs_run-01_dwi.nii.gz /scratch/weishao/rawdata/sub-AVP6176/dwi.nii.gz reading from /scratch/weishao/rawdata/sub-AVP6176/Ses-01/dwi/sub-AVP6176_ses-01_dir-sfs_run-01_dwi.nii.gz... TR=4000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.999608, 0.017447, -0.021891) j_ras = (0.0104682, 0.958258, 0.285714) k_ras = (-0.0259621, -0.285373, 0.958065) writing to /scratch/weishao/rawdata/sub-AVP6176/dwi.nii.gz... #@#--- Eddy/Motion Correct Tue Oct 27 16:19:44 EDT 2020 cd /scratch/weishao/rawdata/sub-AVP6176/ectmp eddy_correct /scratch/weishao/rawdata/sub-AVP6176/dwi.nii.gz /scratch/weishao/rawdata/sub-AVP6176/dwi-ec.nii.gz 0 /cvmfs/ soft.computecanada.ca/easybuild/software/2017/avx2/Compiler/intel2016.4/fsl/5.0.11/fsl/bin/eddy_correct: line 95: /cvmfs/ soft.computecanada.ca/easybuild/software/2017/avx2/Compiler/intel2016.4/fsl/5.0.11/fsl/bin/imglob : *No such file or directory* Usage: fslmerge <-x/y/z/t/a/tr> [tr value in seconds] -t : concatenate images in time -x : concatenate images in the x direction -y : concatenate images in the y direction -z : concatenate images in the z direction -a : auto-choose: single slices -> volume, volumes -> 4D (time series) -tr : concatenate images in time and set the output image tr to the final option value *ERROR: when running eddy_correct* Best, Wei ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Matlab Matlab Runtime issue
External Email - Use Caution HI, There sorry for the late reply, I didn't see the reply due to the email setting issues. I have tried the sudo command, but it still gave me the same error. Best, Wei On Thu, Oct 1, 2020 at 2:56 PM Wei Shao wrote: > Hello, Freesurfer team > > My name is Wei Shao, FS user, I have a few questions regarding the Matlab > package and the hippocampal subfield function with FS. > > I have followed the instruction from the website to install Matlab, sue > the fs_install_mcr R2014b > > (Oct 01, 2020 14:41:05) Exiting with status 0 > (Oct 01, 2020 14:41:05) End - Successful. > Finished > MCR v84 (R2014b) already exists in /usr/local/freesurfer/7.1.0-1 > do you want to reinstall? [y/n] > exiting without install > > *However*, when I try to use the hippocampal seg command: > > *segmentHA_T1.sh, it gives me this error* > > ERROR: cannot find Matlab 2014b runtime in location: > > /usr/local/freesurfer/7.1.0-1/MCRv84 > > The hippocampal/amygdala and brainstem modules require the (free) Matlab > runtime. > You will need to download the Matlab Compiler Runtime (MCR) for Matlab > 2014b. > To do so, please run the following commands (you might need root > permissions): > > LINUX: > > cd /usr/local/freesurfer/7.1.0-1 > curl " > https://surfer.nmr.mgh.harvard.edu/fswiki/MatlabRuntime?action=AttachFile=get=runtime2014bLinux.tar.gz; > -o "runtime2014b.tar.gz" > tar xvf runtime2014b.tar.gz > > Even after I did this as the following, it still gave me the same response > when I tried segmentHA_T1.sh. > > Could you tell me how to fix this? Thanks! > > Best, > Wei > > > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Matlab Matlab Runtime issue
External Email - Use Caution Hello, Freesurfer team My name is Wei Shao, FS user, I have a few questions regarding the Matlab package and the hippocampal subfield function with FS. I have followed the instruction from the website to install Matlab, sue the fs_install_mcr R2014b (Oct 01, 2020 14:41:05) Exiting with status 0 (Oct 01, 2020 14:41:05) End - Successful. Finished MCR v84 (R2014b) already exists in /usr/local/freesurfer/7.1.0-1 do you want to reinstall? [y/n] exiting without install *However*, when I try to use the hippocampal seg command: *segmentHA_T1.sh, it gives me this error* ERROR: cannot find Matlab 2014b runtime in location: /usr/local/freesurfer/7.1.0-1/MCRv84 The hippocampal/amygdala and brainstem modules require the (free) Matlab runtime. You will need to download the Matlab Compiler Runtime (MCR) for Matlab 2014b. To do so, please run the following commands (you might need root permissions): LINUX: cd /usr/local/freesurfer/7.1.0-1 curl " https://surfer.nmr.mgh.harvard.edu/fswiki/MatlabRuntime?action=AttachFile=get=runtime2014bLinux.tar.gz; -o "runtime2014b.tar.gz" tar xvf runtime2014b.tar.gz Even after I did this as the following, it still gave me the same response when I tried segmentHA_T1.sh. Could you tell me how to fix this? Thanks! Best, Wei ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Problem with recon-all command in tutorial dataset
External Email - Use Caution Hi, Freesurfer Team My name is Wei Shao, I just a beginner of Freesurfer. As I play around with the tutorial data, here is a problem I met, I tried to recon-all the dicoms data as the tutorial instruction practice with the date instructed, but it always reports like the SUBJECTS_DIR directory does not exist. [shao@WeiS ~]$ export TUTORIAL_DATA=tutorial_data [shao@WeiS ~]$ export SUBJECTS_DIR=$TUTORIAL_DATA/practice_with_data [shao@WeiS ~]$ cd $SUBJECTS_DIR/dicoms [shao@WeiS dicoms]$ recon-all -all -i I50 -s Subj001 ERROR: SUBJECTS_DIR tutorial_data/practice_with_data does not exist. [shao@WeiS dicoms]$ source $FREESURFER_HOME/SetUpFreeSurfer.sh freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b Setting up environment for FreeSurfer/FS-FAST (and FSL) WARNING: tutorial_data/practice_with_data does not exist FREESURFER_HOME /usr/local/freesurfer/7.1.0-1 FSFAST_HOME /usr/local/freesurfer/7.1.0-1/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR tutorial_data/practice_with_data MNI_DIR /usr/local/freesurfer/7.1.0-1/mni [shao@WeiS dicoms]$ pwd /home/shao/tutorial_data/practice_with_data/dicoms [shao@WeiS dicoms]$ What I should do to fix this problem, Thanks in advance. Best, Wei ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
