[Freesurfer] Labeling of handknob area in primary motor cortex
Dear freesurfer, I was also wondering if you have an existing label of the handknob area located in primary motor cortex? Best, Silas ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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 Partners Compliance HelpLine at http://www.partners.org/complianceline . 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.
[Freesurfer] mri_glmfit skipping .mtx files
Dear freesurfer mailing list, Is there a limit to the number of .mtx files you can feed to mri_glmfit? I am running an anlysis with 25 different .mtx files, and when the analysis runs it just skips the 22nd and 23rd .mtx file. This means these contrasts are also missing from the glmdir. Do you know how I can fix this? -- Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265 neura.edu.au http://neura.edu.au Follow @neuraustralia on twitter https://twitter.com/neuraustraliaFollow NeuRA on facebook https://www.facebook.com/NeuroscienceResearchAustraliaSubscribe to the NeuRA Magazine http://www.neura.edu.au/help-research/subscribe ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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 Partners Compliance HelpLine at http://www.partners.org/complianceline . 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.
[Freesurfer] Labeling of the dorsal part of BA6 (dorsal premotor cortex)
Dear freesurfer, Do you have an existing label of the dorsal part of the premotor cortex? If not, is it possible to manually label this area? Best, Silas ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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 Partners Compliance HelpLine at http://www.partners.org/complianceline . 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.
Re: [Freesurfer] How extract visual areas from non-freesurfer generated Phasemaps?
You can draw ROIs in tksurfer, save them as a label, then use mri_label2vol to map the label into a nifti volume. Why do you need a color wheel for this? On 04/02/2015 06:57 AM, Kaule, Falko wrote: I want to draw a ROI on a surface and save it as nifti (or which type is needed to get there). My original input data is a nifti. For extracting/drawing the visual areas I project the data on a surface. my aim: In the end I want to have nifti from different visual areas to use them as masks for further analysis, i.e. I want to get V1_mask_sub001.nii.gz from the retinotopic mapping of sub001. my current, unspecific way: At the moment I take V1 from the Juelich histological atlas and save it as nifti (using fslview), and align it into subject space. This is quite unspecific, especially since I have the phasemaps for the subjects from retinotopic mapping. the problems (just need to solve one of them): - can't draw and save ROI on inflated in freeview - don't get a colorwheel like colorcode in tksurfer - can't get the nifti aligned to the rtview surface Thank you very much, Falko Date: Wed, 01 Apr 2015 12:43:08 -0400 From: Douglas N Greve gr...@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] How extract visual areas from non-freesurfer generated Phasemaps? To: freesurfer@nmr.mgh.harvard.edu Message-ID: 551c201c.5080...@nmr.mgh.harvard.edu Content-Type: text/plain; charset=windows-1252; format=flowed Hi Falko, I'm not sure what you mean by extract the visual areas as an ROI. Do you want the mean over the ROI? Or each of the time courses? Is your input data a surface or a volume? On 04/01/2015 11:25 AM, Kaule, Falko wrote: Dear all, having phasemaps, generated with AFNI, I would like to extract the visual areas as ROI from a surface view (infalted, flatmap or sth. like this). Steps I've tried: As I'm already familar with freeview and a bit with tksurfer I tried to use them to do that. After reading through the freesurfer-mailinglist and wiki, it seems not possible to extract ROI from surface view. Right? tksurfer can be used to extract i.e. cut, ROI but the colorkey can't be set colorwheel alike. rtview can be used to extract ROI and can have a colorwheel colorcode but expects radian values (sin, cos, and kind of significance values). I converted the phasemaps to sin and cos values. Loading these niftis shows, that the alignment in rtview is wrong. It seems some kind of rotated. The code: # coregister (gives identity matrix because it is already coregistered to anatomy) mov=sub001_pre0_Tstim32_afniPOLpfd_flirt_sin.nii.gz ref=/sub001/templates/t1w/brain.nii.gz reg=new_coreg.dat tkregister2 --s sub001 --targ $ref --mov $mov --regheader --reg $reg # alignment is wrong but colorcode looks as expected rtview --s sub001 --reg $reg --rh --polar --real sub001_pre0_Tstim32_afniPOLpfd_flirt_cos.nii.gz --imag sub001_pre0_Tstim32_afniPOLpfd_flirt_sin.nii.gz --fsig sub001_pre0_Tstim32_afniPOLpfd_flirt_sig.nii.gz # gives proper alignment # tksurfer sub001 rh inflated -overlay pre0_Tstim32_afniPOLpfd_cos.nii.gz -overlay-reg-identity freeview -v sub001/templates/t1w/brain.nii.gz sub001_pre0_Tstim32_afniPOLpfd_flirt_sin.nii.gz:reg=$reg The coregistration matrix new_coreg.dat sub001 0.699928 0.67 0.15 9.99403953552e-01 0.000e+00 1.862645149230957e-09 -1.340251287729188e-06 0.000e+00 9.99403953552e-01 0.000e+00 2.139647040166892e-05 0.000e+00 1.490116119384766e-08 1.000e+00 -2.403078542556614e-05 0 0 0 1 round Thanks, Falko ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this
Re: [Freesurfer] How to extract thickness value of each cluster showed groups difference
That data should already be there. If you run mri_glmfit-sim with --help, look for the description of the csdbase.y.ocn.dat file On 04/02/2015 01:32 PM, yxin-li wrote: Dear Freesurfer expert: I am sorry to disturb you. I am a beginner using freesurfer. I have calcualted the cortical thickness difference between patients and control group using the command mri_glmfit-sim. I found the differences were located in three cluster: cluster1, cluster2 and cluster3. Then I want to extract the thickness value in each cluster and calculate the correlaton between the thickness value and the behavioral performance. Howere I don't know how to achieve this goal. Could anyone give me the example command to produce ROI masks and extract the thickness values. Thanks! Ping Li ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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 Partners Compliance HelpLine at http://www.partners.org/complianceline . 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.
Re: [Freesurfer] mri_glmfit skipping .mtx files
The limit should be 100. If you run mri_glmfit a 2nd time just with the missing contrasts, do they appear? On 04/02/2015 02:34 AM, Bronwyn Overs wrote: Dear freesurfer mailing list, Is there a limit to the number of .mtx files you can feed to mri_glmfit? I am running an anlysis with 25 different .mtx files, and when the analysis runs it just skips the 22nd and 23rd .mtx file. This means these contrasts are also missing from the glmdir. Do you know how I can fix this? -- Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265 neura.edu.au http://neura.edu.au Follow @neuraustralia on twitter https://twitter.com/neuraustraliaFollow NeuRA on facebook https://www.facebook.com/NeuroscienceResearchAustraliaSubscribe to the NeuRA Magazine http://www.neura.edu.au/help-research/subscribe ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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 Partners Compliance HelpLine at http://www.partners.org/complianceline . 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.
Re: [Freesurfer] Label to Nii Conversion
You can use mri_label2label and use the --outmask option. If you are going to use mri_segstats to do the extraction, you can skip the mri_label2label step and specify the label with --slabel (and add --id 1 otherwise it will give you two ROI results, one in the label, the other outside the label) On 04/01/2015 10:50 PM, MCLAREN, Donald wrote: I have a label file on the surface, but want to be able to use it to extract surface data that is already in nifti format (dimensions: [2737 1 6]). Is there a way to convert a label to nifti? Best Regards, Donald McLaren = D.G. McLaren, Ph.D. Research Fellow, Department of Neurology, Massachusetts General Hospital and Harvard Medical School Postdoctoral Research Fellow, GRECC, Bedford VA Website: http://www.martinos.org/~mclaren http://www.martinos.org/%7Emclaren Office: (773) 406-2464 = This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is intended only for the use of the individual or entity named above. If the reader of the e-mail is not the intended recipient or the employee or agent responsible for delivering it to the intended recipient, you are hereby notified that you are in possession of confidential and privileged information. Any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited and may be unlawful. If you have received this e-mail unintentionally, please immediately notify the sender via telephone at (773) 406-2464 or email. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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 Partners Compliance HelpLine at http://www.partners.org/complianceline . 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.
Re: [Freesurfer] mri_watershed Error: indices out of bounds
Hello Edgar, I am going to be looking at your case and seeing if I can replicate the error. I have your .nii file and will run it through our processing stream here, but could you send me your subject folder so that I can look through your files/logs to give me some more information? You can upload the subject folder through filedrop2.0 which is a bit easier to use, as long as your folder is under 2GB! https://gate.nmr.mgh.harvard.edu/filedrop2/ Thank you, Ani Varjabedian On 04/02/2015 11:23 AM, Edgar Busovaca wrote: Hello Bruce, I just wanted to touch base regarding the Indices_oob.nii subject I had sent to MGH. Were you by any chance able to detect the issue with running recon-all on this subject. Thanks in advance for taking a look at this. Best regards, Edgar Busovaca ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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 Partners Compliance HelpLine at http://www.partners.org/complianceline . 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.
Re: [Freesurfer] hello freesurfer developer~
Is dcmdjpeg.fs in your path? What are the contents of the file /tmp/root.tmp.decompressed.dcm.QGcfri.dcmdjpeg.out ? On 04/02/2015 04:53 PM, A-reum Min wrote: Hi doug. I try this as a test. (here is a my terminal) *** [areum@localhost ~]$ su Password: [root@localhost areum]# tcsh [areum@localhost areum]# setenv FREESURFER_HOME /usr/local/freesurfer [areum@localhost areum]# source $FREESURFER_HOME/SetUpFreeSurfer.csh freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer FSFAST_HOME /usr/local/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /usr/local/freesurfer/subjects MNI_DIR /usr/local/freesurfer/mni [areum@localhost areum]# setenv SUBJECTS_DIR /usr/local/freesurfer/subjects/PISA_SPGR/1 [areum@localhost areum]# setenv FS_LOAD_DWI 0 [areum@localhost areum]# mri_convert /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071579.dcm junk.mgh mri_convert /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071579.dcm junk.mgh $Id: mri_convert.c,v 1.219 2015/03/24 17:25:41 greve Exp $ reading from /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071579.dcm... Starting DICOMRead2() dcmfile = /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071579.dcm dcmdir = /usr/local/freesurfer/subjects/PISA_SPGR/1 Ref Series No = 3 Found 246 files, checking for dicoms Found 244 dicom files in series. First Sorting Computing Slice Direction Vs: -0.8 0 0 Vs: -1 0 0 Second Sorting Counting frames nframes = 1 nslices = 244 ndcmfiles = 244 IsDWI = 0 PE Dir = ROW (dicom read) Loading pixel data JPEG compressed, decompressing cd /home/areum dcmdjpeg.fs +te /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071579.dcm /tmp/root.tmp.decompressed.dcm.QGcfri /tmp/root.tmp.decompressed.dcm.QGcfri.dcmdjpeg.out ERROR: 32512, see /tmp/root.tmp.decompressed.dcm.QGcfri.dcmdjpeg.out for more details ** error occured again.. ㅜㅜ when i type the source $FREESURFER_HOME/SetUpFreeSurfer.csh, then show up these freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer FSFAST_HOME /usr/local/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /usr/local/freesurfer/subjects MNI_DIR /usr/local/freesurfer/mni But... my own data directory is /usr/local/freesurfer/subjects/PISA_SPGR/1 so my SUBJECTS_DIR is /usr/local/freesurfer/subjects/PISA_SPGR/1 is it okay...? and i will send my dicom file to u... plz help me as soon as possible ㅜㅜ 2015-04-03 5:02 GMT+09:00 Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu: Can you send me /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071580.dcm ? I might not be able to get to it until after the 13th. Also, try this as a test: setenv FS_LOAD_DWI 0 mri_convert /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071580.dcm junk.mgh If that works, you can set that environment variable and run recon-all. But if you can send me the dicom above I'd appreciate it. doug On 04/02/2015 01:40 AM, A-reum Min wrote: hi doug recon is still not working... if i type the recon-all -i /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071579.dcm -i /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071580.dcm -all -s subj001 then error occured ++ ERROR: GetDICOMInfo(): dcmGetDWIParams() 7 DICOM File: /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071580.dcm ERROR: GetDICOMInfo(): dcmGetDWIParams() 7 DICOM File: /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071581.dcm ERROR: GetDICOMInfo(): dcmGetDWIParams() 7 DICOM File: /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071582.dcm ERROR: GetDICOMInfo(): dcmGetDWIParams() 7 DICOM File: /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071583.dcm ERROR: GetDICOMInfo(): dcmGetDWIParams() 7 DICOM File: /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071584.dcm ERROR: GetDICOMInfo(): dcmGetDWIParams() 7 DICOM File: /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071585.dcm ERROR: GetDICOMInfo(): dcmGetDWIParams() 7 DICOM File: /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071586.dcm ERROR: GetDICOMInfo(): dcmGetDWIParams() 7 DICOM File: /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071587.dcm ERROR: GetDICOMInfo(): dcmGetDWIParams() 7 DICOM File: /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071588.dcm ERROR: GetDICOMInfo():
Re: [Freesurfer] hello freesurfer developer~
I click the /tmp/root.tmp.decompressed.dcm.QGcfri.dcmdjpeg.out file. and then show up these dcmdjpeg.fs: error while loading shared libraries: libdcmjpeg.so.3.6: cannot open shared object file: No such file or directory dcmdjpeg.fs path is /usr/local/freesurfer/bin (FREESURFER_HOME/bin) and my subjects path(own data) /usr/local/freesurfer/subjects/PISA_SPGR/1 --SUBJECTS_DIR 2015-04-03 10:50 GMT+09:00 A-reum Min naniy...@gmail.com: I click the /tmp/root.tmp.decompressed.dcm.QGcfri.dcmdjpeg.out file. and then show up these dcmdjpeg.fs: error while loading shared libraries: libdcmjpeg.so.3.6: cannot open shared object file: No such file or directory dcmjpeg.fs path is /usr/local/freesurfer/bin (FREESURFER_HOME/bin) and my subjects path(own data) /usr/local/freesurfer/subjects/PISA_SPGR/1 --SUBJECTS_DIR 2015-04-03 7:02 GMT+09:00 Douglas N Greve gr...@nmr.mgh.harvard.edu: Is dcmdjpeg.fs in your path? What are the contents of the file /tmp/root.tmp.decompressed.dcm.QGcfri.dcmdjpeg.out ? On 04/02/2015 04:53 PM, A-reum Min wrote: Hi doug. I try this as a test. (here is a my terminal) *** [areum@localhost ~]$ su Password: [root@localhost areum]# tcsh [areum@localhost areum]# setenv FREESURFER_HOME /usr/local/freesurfer [areum@localhost areum]# source $FREESURFER_HOME/SetUpFreeSurfer.csh freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer FSFAST_HOME /usr/local/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /usr/local/freesurfer/subjects MNI_DIR /usr/local/freesurfer/mni [areum@localhost areum]# setenv SUBJECTS_DIR /usr/local/freesurfer/subjects/PISA_SPGR/1 [areum@localhost areum]# setenv FS_LOAD_DWI 0 [areum@localhost areum]# mri_convert /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071579.dcm junk.mgh mri_convert /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071579.dcm junk.mgh $Id: mri_convert.c,v 1.219 2015/03/24 17:25:41 greve Exp $ reading from /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071579.dcm... Starting DICOMRead2() dcmfile = /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071579.dcm dcmdir = /usr/local/freesurfer/subjects/PISA_SPGR/1 Ref Series No = 3 Found 246 files, checking for dicoms Found 244 dicom files in series. First Sorting Computing Slice Direction Vs: -0.8 0 0 Vs: -1 0 0 Second Sorting Counting frames nframes = 1 nslices = 244 ndcmfiles = 244 IsDWI = 0 PE Dir = ROW (dicom read) Loading pixel data JPEG compressed, decompressing cd /home/areum dcmdjpeg.fs +te /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071579.dcm /tmp/root.tmp.decompressed.dcm.QGcfri /tmp/root.tmp.decompressed.dcm.QGcfri.dcmdjpeg.out ERROR: 32512, see /tmp/root.tmp.decompressed.dcm.QGcfri.dcmdjpeg.out for more details ** error occured again.. ㅜㅜ when i type the source $FREESURFER_HOME/SetUpFreeSurfer.csh, then show up these freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer FSFAST_HOME /usr/local/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /usr/local/freesurfer/subjects MNI_DIR /usr/local/freesurfer/mni But... my own data directory is /usr/local/freesurfer/subjects/PISA_SPGR/1 so my SUBJECTS_DIR is /usr/local/freesurfer/subjects/PISA_SPGR/1 is it okay...? and i will send my dicom file to u... plz help me as soon as possible ㅜㅜ 2015-04-03 5:02 GMT+09:00 Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu: Can you send me /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071580.dcm ? I might not be able to get to it until after the 13th. Also, try this as a test: setenv FS_LOAD_DWI 0 mri_convert /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071580.dcm junk.mgh If that works, you can set that environment variable and run recon-all. But if you can send me the dicom above I'd appreciate it. doug On 04/02/2015 01:40 AM, A-reum Min wrote: hi doug recon is still not working... if i type the recon-all -i /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071579.dcm -i /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071580.dcm -all -s subj001 then error occured ++ ERROR: GetDICOMInfo(): dcmGetDWIParams() 7 DICOM File: /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071580.dcm ERROR:
Re: [Freesurfer] hello freesurfer developer~
I click the /tmp/root.tmp.decompressed.dcm.QGcfri.dcmdjpeg.out file. and then show up these dcmdjpeg.fs: error while loading shared libraries: libdcmjpeg.so.3.6: cannot open shared object file: No such file or directory dcmjpeg.fs path is /usr/local/freesurfer/bin (FREESURFER_HOME/bin) and my subjects path(own data) /usr/local/freesurfer/subjects/PISA_SPGR/1 --SUBJECTS_DIR 2015-04-03 7:02 GMT+09:00 Douglas N Greve gr...@nmr.mgh.harvard.edu: Is dcmdjpeg.fs in your path? What are the contents of the file /tmp/root.tmp.decompressed.dcm.QGcfri.dcmdjpeg.out ? On 04/02/2015 04:53 PM, A-reum Min wrote: Hi doug. I try this as a test. (here is a my terminal) *** [areum@localhost ~]$ su Password: [root@localhost areum]# tcsh [areum@localhost areum]# setenv FREESURFER_HOME /usr/local/freesurfer [areum@localhost areum]# source $FREESURFER_HOME/SetUpFreeSurfer.csh freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer FSFAST_HOME /usr/local/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /usr/local/freesurfer/subjects MNI_DIR /usr/local/freesurfer/mni [areum@localhost areum]# setenv SUBJECTS_DIR /usr/local/freesurfer/subjects/PISA_SPGR/1 [areum@localhost areum]# setenv FS_LOAD_DWI 0 [areum@localhost areum]# mri_convert /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071579.dcm junk.mgh mri_convert /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071579.dcm junk.mgh $Id: mri_convert.c,v 1.219 2015/03/24 17:25:41 greve Exp $ reading from /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071579.dcm... Starting DICOMRead2() dcmfile = /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071579.dcm dcmdir = /usr/local/freesurfer/subjects/PISA_SPGR/1 Ref Series No = 3 Found 246 files, checking for dicoms Found 244 dicom files in series. First Sorting Computing Slice Direction Vs: -0.8 0 0 Vs: -1 0 0 Second Sorting Counting frames nframes = 1 nslices = 244 ndcmfiles = 244 IsDWI = 0 PE Dir = ROW (dicom read) Loading pixel data JPEG compressed, decompressing cd /home/areum dcmdjpeg.fs +te /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071579.dcm /tmp/root.tmp.decompressed.dcm.QGcfri /tmp/root.tmp.decompressed.dcm.QGcfri.dcmdjpeg.out ERROR: 32512, see /tmp/root.tmp.decompressed.dcm.QGcfri.dcmdjpeg.out for more details ** error occured again.. ㅜㅜ when i type the source $FREESURFER_HOME/SetUpFreeSurfer.csh, then show up these freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer FSFAST_HOME /usr/local/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /usr/local/freesurfer/subjects MNI_DIR /usr/local/freesurfer/mni But... my own data directory is /usr/local/freesurfer/subjects/PISA_SPGR/1 so my SUBJECTS_DIR is /usr/local/freesurfer/subjects/PISA_SPGR/1 is it okay...? and i will send my dicom file to u... plz help me as soon as possible ㅜㅜ 2015-04-03 5:02 GMT+09:00 Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu: Can you send me /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071580.dcm ? I might not be able to get to it until after the 13th. Also, try this as a test: setenv FS_LOAD_DWI 0 mri_convert /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071580.dcm junk.mgh If that works, you can set that environment variable and run recon-all. But if you can send me the dicom above I'd appreciate it. doug On 04/02/2015 01:40 AM, A-reum Min wrote: hi doug recon is still not working... if i type the recon-all -i /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071579.dcm -i /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071580.dcm -all -s subj001 then error occured ++ ERROR: GetDICOMInfo(): dcmGetDWIParams() 7 DICOM File: /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071580.dcm ERROR: GetDICOMInfo(): dcmGetDWIParams() 7 DICOM File: /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071581.dcm ERROR: GetDICOMInfo(): dcmGetDWIParams() 7 DICOM File: /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071582.dcm ERROR: GetDICOMInfo(): dcmGetDWIParams() 7 DICOM File: /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071583.dcm ERROR: GetDICOMInfo(): dcmGetDWIParams() 7 DICOM File:
Re: [Freesurfer] hello freesurfer developer~
Hi doug dcmdjpeg.fs path is /usr/local/freesurfer/bin (FREESURFER_HOME/bin) I click the /tmp/root.tmp.decompressed.dcm.QGcfri.dcmdjpeg.out file. and then show up these dcmdjpeg.fs: error while loading shared libraries: libdcmjpeg.so.3.6: cannot open shared object file: No such file or directory always error in tmp file(x signed root.tmp.decompressed.dcm.000). so, fix the x signed root.tmp.decompressed files... and i have no libdcmjpeg.so.3.6.. i need it. 2015-04-03 7:02 GMT+09:00 Douglas N Greve gr...@nmr.mgh.harvard.edu: Is dcmdjpeg.fs in your path? What are the contents of the file /tmp/root.tmp.decompressed.dcm.QGcfri.dcmdjpeg.out ? On 04/02/2015 04:53 PM, A-reum Min wrote: Hi doug. I try this as a test. (here is a my terminal) *** [areum@localhost ~]$ su Password: [root@localhost areum]# tcsh [areum@localhost areum]# setenv FREESURFER_HOME /usr/local/freesurfer [areum@localhost areum]# source $FREESURFER_HOME/SetUpFreeSurfer.csh freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer FSFAST_HOME /usr/local/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /usr/local/freesurfer/subjects MNI_DIR /usr/local/freesurfer/mni [areum@localhost areum]# setenv SUBJECTS_DIR /usr/local/freesurfer/subjects/PISA_SPGR/1 [areum@localhost areum]# setenv FS_LOAD_DWI 0 [areum@localhost areum]# mri_convert /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071579.dcm junk.mgh mri_convert /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071579.dcm junk.mgh $Id: mri_convert.c,v 1.219 2015/03/24 17:25:41 greve Exp $ reading from /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071579.dcm... Starting DICOMRead2() dcmfile = /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071579.dcm dcmdir = /usr/local/freesurfer/subjects/PISA_SPGR/1 Ref Series No = 3 Found 246 files, checking for dicoms Found 244 dicom files in series. First Sorting Computing Slice Direction Vs: -0.8 0 0 Vs: -1 0 0 Second Sorting Counting frames nframes = 1 nslices = 244 ndcmfiles = 244 IsDWI = 0 PE Dir = ROW (dicom read) Loading pixel data JPEG compressed, decompressing cd /home/areum dcmdjpeg.fs +te /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071579.dcm /tmp/root.tmp.decompressed.dcm.QGcfri /tmp/root.tmp.decompressed.dcm.QGcfri.dcmdjpeg.out ERROR: 32512, see /tmp/root.tmp.decompressed.dcm.QGcfri.dcmdjpeg.out for more details ** error occured again.. ㅜㅜ when i type the source $FREESURFER_HOME/SetUpFreeSurfer.csh, then show up these freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer FSFAST_HOME /usr/local/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /usr/local/freesurfer/subjects MNI_DIR /usr/local/freesurfer/mni But... my own data directory is /usr/local/freesurfer/subjects/PISA_SPGR/1 so my SUBJECTS_DIR is /usr/local/freesurfer/subjects/PISA_SPGR/1 is it okay...? and i will send my dicom file to u... plz help me as soon as possible ㅜㅜ 2015-04-03 5:02 GMT+09:00 Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu: Can you send me /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071580.dcm ? I might not be able to get to it until after the 13th. Also, try this as a test: setenv FS_LOAD_DWI 0 mri_convert /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071580.dcm junk.mgh If that works, you can set that environment variable and run recon-all. But if you can send me the dicom above I'd appreciate it. doug On 04/02/2015 01:40 AM, A-reum Min wrote: hi doug recon is still not working... if i type the recon-all -i /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071579.dcm -i /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071580.dcm -all -s subj001 then error occured ++ ERROR: GetDICOMInfo(): dcmGetDWIParams() 7 DICOM File: /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071580.dcm ERROR: GetDICOMInfo(): dcmGetDWIParams() 7 DICOM File: /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071581.dcm ERROR: GetDICOMInfo(): dcmGetDWIParams() 7 DICOM File: /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071582.dcm ERROR: GetDICOMInfo(): dcmGetDWIParams() 7 DICOM File: /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071583.dcm ERROR:
Re: [Freesurfer] Labeling of the dorsal part of BA6 (dorsal premotor cortex)
Hi Silas sure, there are tools for drawing ROIs/labels on the surface in tksurfer. You can create a label on fsaverage or an individual subject, then use mri_label2label to map it to other subjects if you like cheers Bruce On Thu, 2 Apr 2015, Silas wrote: Dear freesurfer, Do you have an existing label of the dorsal part of the premotor cortex? If not, is it possible to manually label this area? Best, Silas ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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 Partners Compliance HelpLine at http://www.partners.org/complianceline . 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.
Re: [Freesurfer] How extract visual areas from non-freesurfer generated Phasemaps?
Hi Falko why not use our estimates of V1/V2 instead? They are far more accurate. I think tksurfer has a colorwheel option, since we always used it for retinotopy analysis way back when. But even if not, you should be able to create the label in tksurfer then import it into freeview, no? cheers Bruce On Thu, 2 Apr 2015, Kaule, Falko wrote: I want to draw a ROI on a surface and save it as nifti (or which type is needed to get there). My original input data is a nifti. For extracting/drawing the visual areas I project the data on a surface. my aim: In the end I want to have nifti from different visual areas to use them as masks for further analysis, i.e. I want to get V1_mask_sub001.nii.gz from the retinotopic mapping of sub001. my current, unspecific way: At the moment I take V1 from the Juelich histological atlas and save it as nifti (using fslview), and align it into subject space. This is quite unspecific, especially since I have the phasemaps for the subjects from retinotopic mapping. the problems (just need to solve one of them): - can't draw and save ROI on inflated in freeview - don't get a colorwheel like colorcode in tksurfer - can't get the nifti aligned to the rtview surface Thank you very much, Falko Date: Wed, 01 Apr 2015 12:43:08 -0400 From: Douglas N Greve gr...@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] How extract visual areas from non-freesurfer generated Phasemaps? To: freesurfer@nmr.mgh.harvard.edu Message-ID: 551c201c.5080...@nmr.mgh.harvard.edu Content-Type: text/plain; charset=windows-1252; format=flowed Hi Falko, I'm not sure what you mean by extract the visual areas as an ROI. Do you want the mean over the ROI? Or each of the time courses? Is your input data a surface or a volume? On 04/01/2015 11:25 AM, Kaule, Falko wrote: Dear all, having phasemaps, generated with AFNI, I would like to extract the visual areas as ROI from a surface view (infalted, flatmap or sth. like this). Steps I've tried: As I'm already familar with freeview and a bit with tksurfer I tried to use them to do that. After reading through the freesurfer-mailinglist and wiki, it seems not possible to extract ROI from surface view. Right? tksurfer can be used to extract i.e. cut, ROI but the colorkey can't be set colorwheel alike. rtview can be used to extract ROI and can have a colorwheel colorcode but expects radian values (sin, cos, and kind of significance values). I converted the phasemaps to sin and cos values. Loading these niftis shows, that the alignment in rtview is wrong. It seems some kind of rotated. The code: # coregister (gives identity matrix because it is already coregistered to anatomy) mov=sub001_pre0_Tstim32_afniPOLpfd_flirt_sin.nii.gz ref=/sub001/templates/t1w/brain.nii.gz reg=new_coreg.dat tkregister2 --s sub001 --targ $ref --mov $mov --regheader --reg $reg # alignment is wrong but colorcode looks as expected rtview --s sub001 --reg $reg --rh --polar --real sub001_pre0_Tstim32_afniPOLpfd_flirt_cos.nii.gz --imag sub001_pre0_Tstim32_afniPOLpfd_flirt_sin.nii.gz --fsig sub001_pre0_Tstim32_afniPOLpfd_flirt_sig.nii.gz # gives proper alignment # tksurfer sub001 rh inflated -overlay pre0_Tstim32_afniPOLpfd_cos.nii.gz -overlay-reg-identity freeview -v sub001/templates/t1w/brain.nii.gz sub001_pre0_Tstim32_afniPOLpfd_flirt_sin.nii.gz:reg=$reg The coregistration matrix new_coreg.dat sub001 0.699928 0.67 0.15 9.99403953552e-01 0.000e+00 1.862645149230957e-09 -1.340251287729188e-06 0.000e+00 9.99403953552e-01 0.000e+00 2.139647040166892e-05 0.000e+00 1.490116119384766e-08 1.000e+00 -2.403078542556614e-05 0 0 0 1 round Thanks, Falko ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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 Partners Compliance
Re: [Freesurfer] Labeling of handknob area in primary motor cortex
no, I don't think we do sorry Bruce On Thu, 2 Apr 2015, Silas wrote: Dear freesurfer, I was also wondering if you have an existing label of the handknob area located in primary motor cortex? Best, Silas ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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 Partners Compliance HelpLine at http://www.partners.org/complianceline . 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.
Re: [Freesurfer] How extract visual areas from non-freesurfer generated Phasemaps?
I want to draw a ROI on a surface and save it as nifti (or which type is needed to get there). My original input data is a nifti. For extracting/drawing the visual areas I project the data on a surface. my aim: In the end I want to have nifti from different visual areas to use them as masks for further analysis, i.e. I want to get V1_mask_sub001.nii.gz from the retinotopic mapping of sub001. my current, unspecific way: At the moment I take V1 from the Juelich histological atlas and save it as nifti (using fslview), and align it into subject space. This is quite unspecific, especially since I have the phasemaps for the subjects from retinotopic mapping. the problems (just need to solve one of them): - can't draw and save ROI on inflated in freeview - don't get a colorwheel like colorcode in tksurfer - can't get the nifti aligned to the rtview surface Thank you very much, Falko Date: Wed, 01 Apr 2015 12:43:08 -0400 From: Douglas N Greve gr...@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] How extract visual areas from non-freesurfer generated Phasemaps? To: freesurfer@nmr.mgh.harvard.edu Message-ID: 551c201c.5080...@nmr.mgh.harvard.edu Content-Type: text/plain; charset=windows-1252; format=flowed Hi Falko, I'm not sure what you mean by extract the visual areas as an ROI. Do you want the mean over the ROI? Or each of the time courses? Is your input data a surface or a volume? On 04/01/2015 11:25 AM, Kaule, Falko wrote: Dear all, having phasemaps, generated with AFNI, I would like to extract the visual areas as ROI from a surface view (infalted, flatmap or sth. like this). Steps I've tried: As I'm already familar with freeview and a bit with tksurfer I tried to use them to do that. After reading through the freesurfer-mailinglist and wiki, it seems not possible to extract ROI from surface view. Right? tksurfer can be used to extract i.e. cut, ROI but the colorkey can't be set colorwheel alike. rtview can be used to extract ROI and can have a colorwheel colorcode but expects radian values (sin, cos, and kind of significance values). I converted the phasemaps to sin and cos values. Loading these niftis shows, that the alignment in rtview is wrong. It seems some kind of rotated. The code: # coregister (gives identity matrix because it is already coregistered to anatomy) mov=sub001_pre0_Tstim32_afniPOLpfd_flirt_sin.nii.gz ref=/sub001/templates/t1w/brain.nii.gz reg=new_coreg.dat tkregister2 --s sub001 --targ $ref --mov $mov --regheader --reg $reg # alignment is wrong but colorcode looks as expected rtview --s sub001 --reg $reg --rh --polar --real sub001_pre0_Tstim32_afniPOLpfd_flirt_cos.nii.gz --imag sub001_pre0_Tstim32_afniPOLpfd_flirt_sin.nii.gz --fsig sub001_pre0_Tstim32_afniPOLpfd_flirt_sig.nii.gz # gives proper alignment # tksurfer sub001 rh inflated -overlay pre0_Tstim32_afniPOLpfd_cos.nii.gz -overlay-reg-identity freeview -v sub001/templates/t1w/brain.nii.gz sub001_pre0_Tstim32_afniPOLpfd_flirt_sin.nii.gz:reg=$reg The coregistration matrix new_coreg.dat sub001 0.699928 0.67 0.15 9.99403953552e-01 0.000e+00 1.862645149230957e-09 -1.340251287729188e-06 0.000e+00 9.99403953552e-01 0.000e+00 2.139647040166892e-05 0.000e+00 1.490116119384766e-08 1.000e+00 -2.403078542556614e-05 0 0 0 1 round Thanks, Falko ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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 Partners Compliance HelpLine at http://www.partners.org/complianceline . 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.
[Freesurfer] R: Re: isxconcat-sess problem
Thank you very much. I have resolved Sess49 (--s) error but the ERROR: Flag —s unrecognized is still remained. Stefano Messaggio originale Da: gr...@nmr.mgh.harvard.edu Data: 31-mar-2015 18.07 A: freesurfer@nmr.mgh.harvard.edu Ogg: Re: [Freesurfer] isxconcat-sess problem Not sure what is going wrong with the 1st cmd, but the 2nd has a double dash just before Sess49 (--s) that is causing the problem doug On 03/31/2015 07:55 AM, std...@virgilio.it wrote: Hi list, I'm performing the FS-FAST analysis. Some months ago, I have already preformed this analysis on some subjects without problem. Now, I have added some subjects. When I rerun the analysis i have these error: for isxconcat-sess -sf sessidlist —analysis fc.lthalseed.surf.lh -contrast L_Thalamus -o my-group_thal_LH ERROR: finding sessions Sess47 /Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess15 /Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess48 /Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess49 /Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess50 [iMac-di-Stefano:freesurfer/subjects/FUNCTIONAL_DATA] Stefano% and for isxconcat-sess -s Sess01 -s Sess02 -s Sess03 -s Sess04 -s Sess05 -s Sess06 -s Sess07 -s Sess08 -s Sess09 -s Sess10 -s Sess11 -s Sess12 -s Sess13 —s Sess14 -s Sess15 -s Sess16 -s Sess30 -s Sess31 -s Sess32 -s Sess33 -s Sess34 -s Sess35 -s Sess36 -s Sess37 -s Sess39 -s Sess40 -s Sess41 -s Sess42 -s Sess43 -s Sess44 -s Sess45 -s Sess46 -s Sess47 -s Sess48 —s Sess49 -s Sess50 —analysis fc.lthalseed.surf.lh -contrast L_Thalamus -o my-group_THAL_LEFT ERROR: Flag —s unrecognized. FUNCTIONAL_DATA directory contains: file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/fc.lamgseed.surf.lh/ file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/fc.lthalseed.surf.lh/ file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/fc.ramgseed.surf.rh/ file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/fc.rthalseed.surf.rh/ file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/file.fsgd file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/g1g2.intercept.mtx file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/group.diff.mtx file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/group1.mtx file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/group2.mtx file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/GroupDescriptorFile%201 file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/log/ file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/mean.L_Amygdala.config file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/mean.L_Thalamus.config file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/mean.R_Amygdala.config file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/mean.R_Thalamus.config file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess01/ file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess02/ file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess03/ file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess04/ file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess05/ file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess06/ file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess07/ file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess08/ file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess09/ file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess10/ file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess11/ file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess12/ file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess13/ file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess14/ file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess15/ file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess16/ file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess30/ file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess31/ file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess32/ file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess33/ file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess34/ file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess35/ file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess36/ file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess37/ file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess39/ file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess40/ file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess41/ file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess42/ file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess43/ file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess44/ file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess45/ file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess46/
Re: [Freesurfer] R: Re: isxconcat-sess problem
do you have another double dash (--s) in the command line? On 4/3/15 1:00 AM, std...@virgilio.it wrote: Thank you very much. I have resolved Sess49 (--s) error but the ERROR: Flag —s unrecognized is still remained. Stefano Messaggio originale Da: gr...@nmr.mgh.harvard.edu Data: 31-mar-2015 18.07 A: freesurfer@nmr.mgh.harvard.edu Ogg: Re: [Freesurfer] isxconcat-sess problem Not sure what is going wrong with the 1st cmd, but the 2nd has a double dash just before Sess49 (--s) that is causing the problem doug On 03/31/2015 07:55 AM, std...@virgilio.it wrote: Hi list, I'm performing the FS-FAST analysis. Some months ago, I have already preformed this analysis on some subjects without problem. Now, I have added some subjects. When I rerun the analysis i have these error: for isxconcat-sess -sf sessidlist —analysis fc.lthalseed.surf.lh -contrast L_Thalamus -o my-group_thal_LH ERROR: finding sessions Sess47 /Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess15 /Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess48 /Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess49 /Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess50 [iMac-di-Stefano:freesurfer/subjects/FUNCTIONAL_DATA] Stefano% and for isxconcat-sess -s Sess01 -s Sess02 -s Sess03 -s Sess04 -s Sess05 -s Sess06 -s Sess07 -s Sess08 -s Sess09 -s Sess10 -s Sess11 -s Sess12 -s Sess13 —s Sess14 -s Sess15 -s Sess16 -s Sess30 -s Sess31 -s Sess32 -s Sess33 -s Sess34 -s Sess35 -s Sess36 -s Sess37 -s Sess39 -s Sess40 -s Sess41 -s Sess42 -s Sess43 -s Sess44 -s Sess45 -s Sess46 -s Sess47 -s Sess48 —s Sess49 -s Sess50 —analysis fc.lthalseed.surf.lh -contrast L_Thalamus -o my-group_THAL_LEFT ERROR: Flag —s unrecognized. FUNCTIONAL_DATA directory contains: file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/fc.lamgseed.surf.lh/ file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/fc.lthalseed.surf.lh/ file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/fc.ramgseed.surf.rh/ file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/fc.rthalseed.surf.rh/ file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/file.fsgd file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/g1g2.intercept.mtx file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/group.diff.mtx file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/group1.mtx file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/group2.mtx file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/GroupDescriptorFile%201 file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/log/ file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/mean.L_Amygdala.config file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/mean.L_Thalamus.config file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/mean.R_Amygdala.config file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/mean.R_Thalamus.config file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess01/ file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess02/ file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess03/ file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess04/ file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess05/ file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess06/ file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess07/ file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess08/ file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess09/ file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess10/ file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess11/ file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess12/ file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess13/ file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess14/ file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess15/ file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess16/ file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess30/ file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess31/ file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess32/ file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess33/ file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess34/ file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess35/ file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess36/ file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess37/ file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess39/ file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess40/ file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess41/ file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess42/ file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess43/ file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess44/ file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess45/
[Freesurfer] mri glmfit-sim (group analysis tutorial question)
Dear all, I am following the tutorial for group analysis. I successfully ran all the steps up until the simulation for clusterwise correction. When I attempted to run the mri_glmfit-sim using the following command in the tutorial: mri_glmfit-sim \ --glmdir lh.gender_age.glmdir \ --cache 4 neg \ --cwp 0.05\ --2spaces I receive the following error: ERROR: cannot find /autofs/cluster/birn/LEGACY/45/users/BWH/buckner_data/tutorial_subjs/group_analysis_tutorial/glm Do you know how can I go about addressing this issue? Thank you. Best regards, Ece -- Özlem Ece Demir, Ph.D. Research Director Language Development Project Department of Psychology University of Chicago 5848 South University Avenue Chicago, IL 60637 Telephone: 773-732-7144 Fax: 773-834-5261 Email: e...@uchicago.edu ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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 Partners Compliance HelpLine at http://www.partners.org/complianceline . 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.
Re: [Freesurfer] mri_watershed Error: indices out of bounds
Hello Bruce, I just wanted to touch base regarding the Indices_oob.nii subject I had sent to MGH. Were you by any chance able to detect the issue with running recon-all on this subject. Thanks in advance for taking a look at this. Best regards, Edgar Busovaca ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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 Partners Compliance HelpLine at http://www.partners.org/complianceline . 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.
[Freesurfer] Talairach coordinate discrepancy mri_surfcluster vs tksurfer
Hi Doug and Freesurfers, I ran mri_surfcluster to generate coordinates for cluster maxima from a functional surface analysis. The summary text file generated by mri_surfcluster lists a bunch of information about the clusters, including talairach coordinates for each cluster peak (see example below). I visualized these max vertices in tksurfer by entering the VtxMax given in the summary file into the Vertex Index field in the tksurfer tools window. I'm noticing, however, that the talairach coordinates given in the tksurfer tools window (Vertex Talairach) after entering the vertex index are not the same as the coordinates listed in the summary file. Seems the coordinates are off by .5 - 1 millimeter or so, which I know is not much, but I'm curious if anyone knows the reason for this discrepancy? Additionally, if we want to use the peaks for seeds in a functional connectivity analysis which set of coordinates is more accurate? Any insight would be greatly appreciated! Best, Alex Ex. Summary text file: # ClusterNo Max VtxMax Size(mm^2) TalX TalY TalZNVtxs 1 33.019 124877 1219.98 30.7 21.1 -1.4 2841 2 27.538 116676 1406.49 7.6 23.7 38.1 2923 3 25.380 109387 3977.58 41.9 31.2 26.7 7023 4 24.404 86863 3241.21 31.5 -60.2 39.0 7288 5 -20.441 104109 1903.13 5.5 20.5 -7.4 3923 6 18.118 141781600.75 5.5 -23.0 26.4 1553 Cluster 1 Vertex Talairach coordinates from tksurfer tools: (29.88 20.79 -1.32) ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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 Partners Compliance HelpLine at http://www.partners.org/complianceline . 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.
[Freesurfer] How to extract thickness value of each cluster showed groups difference
Dear Freesurfer expert: I am sorry to disturb you. I am a beginner using freesurfer. I have calcualted the cortical thickness difference between patients and control group using the command mri_glmfit-sim. I found the differences were located in three cluster: cluster1, cluster2 and cluster3. Then I want to extract the thickness value in each cluster and calculate the correlaton between the thickness value and the behavioral performance. Howere I don't know how to achieve this goal. Could anyone give me the example command to produce ROI masks and extract the thickness values. Thanks! Ping Li___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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 Partners Compliance HelpLine at http://www.partners.org/complianceline . 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.
[Freesurfer] Brain Imaging, Built Better: The HCP Course in Hawaii
To advance the field of brain imaging, the HCP was given the unusual NIH mandate to devote its first two years to rethinking data acquisition and analysis methods prior to collecting its core dataset. The HCP course provides an excellent opportunity for brain imagers to profit from this experience by interacting with key HCP investigators in an accessible and approachable setting. Among the speakers are David Van Essen (HCP¹s PI), Steve Smith (FSL), Tom Nichols (brain imaging statistician), Dan Marcus (XNAT and ConnectomeDB), Robert Oostenveld (FieldTrip), and many others. We¹ve designed the HCP Course both for folks with considerable brain imaging experience and for those who are just starting out. Attendees will learn how to take advantage of HCP-related advances in data acquisition, preprocessing, and analysis methods, enhancing their prospects in an increasingly competitive neuroimaging field. Highlighted topics include: *How to acquire high quality MRI data for use with the HCP¹s cutting-edge analysis tools. *How to better answer the question ³Where am I in the brain?² by using the HCP¹s new standard space and analysis approachCIFTI grayordinatesthat substantially improves spatial localization across subjects and studies. *How to avoid the erosion of neuroanatomical fidelity caused by conventional brain imaging analysis methods, instead accurately aligning cortical areas across subjects and studies and minimizing blurring. *The first public unveiling of the HCP¹s group average multi-modal cortical parcellation together with methods for automatically defining these parcels in individual subjectseven those with atypical cortical organization. *How to perform novel analyses by integrating very high temporal resolution electrophysiological data (MEG) together with high spatial resolution MRI in a common analysis framework built around parcellation. Note that space is limitedand who doesn¹t want an excuse join us in Hawaii for an extra week before OHBM? (June 8-12) See the HCP course website for more details and let us know if you have any questions (hcpcou...@humanconnectome.org): http://humanconnectome.org/course-registration/2015/exploring-the-human-con nectome.php Hope to see you in Honolulu, Matt Glasser. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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 Partners Compliance HelpLine at http://www.partners.org/complianceline . 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.
[Freesurfer] Computing pial layers
Hi Freesurfers, I'm having some trouble computing the pial layers. Below are the details. Thanks! Here is the output from bugr: FREESURFER_HOME: /usr/local/freesurfer/stable5_3_0 Build stamp: freesurfer-Linux-centos6_x86_64-stable-v5.3.0-20130514 RedHat release: CentOS release 6.5 (Final) Kernel info: Linux 2.6.32-431.20.3.el6.x86_64 x86_64 NMR Center info (/space/freesurfer exists): machine: huygens SUBJECTS_DIR: /autofs/space/huygens_001/users/mia/subjects PWD: /autofs/space/huygens_001/users/mia/subjects/MG82_SurferOutput_CT3/surf ssh huygens setenv SUBJECTS_DIR /autofs/space/huygens_001/users/mia/subjects cd /autofs/space/huygens_001/users/mia/subjects/MG82_SurferOutput_CT3/surf 1) MG82 2) mris_compute_lgi --i lh.pial --close_sphere_size 30 --smooth_iters 60 3) Error in dsearchn (line 79) [d(i),t(i)] = min(sum((x-yi).^2,2)); Error in mesh_vertex_nearest (line 29) nearestIndex = dsearchn(vertices,points); Error in reorganize_verticeslist (line 28) [nextindex,nextvalue]=mesh_vertex_nearest(mesh_total.vertices(remaininglist,:),mesh_total.vertices(verticeslist(start_vertex),:)); Error in make_roi_paths (line 93) reorglist = reorganize_verticeslist (mesh_total, A, mesh_outer, perim, verticeslist, step); ERROR: make_roi_paths did not complete successfully! ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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 Partners Compliance HelpLine at http://www.partners.org/complianceline . 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.
Re: [Freesurfer] mri glmfit-sim (group analysis tutorial question)
Did you run mri_glmfit before that to create lh.gender_age.glmdir ? On 04/02/2015 12:08 PM, Özlem Ece Demir wrote: Dear all, I am following the tutorial for group analysis. I successfully ran all the steps up until the simulation for clusterwise correction. When I attempted to run the mri_glmfit-sim using the following command in the tutorial: mri_glmfit-sim \ --glmdir lh.gender_age.glmdir \ --cache 4 neg \ --cwp 0.05\ --2spaces I receive the following error: ERROR: cannot find /autofs/cluster/birn/LEGACY/45/users/BWH/buckner_data/tutorial_subjs/group_analysis_tutorial/glm Do you know how can I go about addressing this issue? Thank you. Best regards, Ece -- Özlem Ece Demir, Ph.D. Research Director Language Development Project Department of Psychology University of Chicago 5848 South University Avenue Chicago, IL 60637 Telephone: 773-732-7144 Fax: 773-834-5261 Email: e...@uchicago.edu mailto:e...@uchicago.edu ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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 Partners Compliance HelpLine at http://www.partners.org/complianceline . 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.
Re: [Freesurfer] hello freesurfer developer~
Can you send me /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071580.dcm ? I might not be able to get to it until after the 13th. Also, try this as a test: setenv FS_LOAD_DWI 0 mri_convert /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071580.dcm junk.mgh If that works, you can set that environment variable and run recon-all. But if you can send me the dicom above I'd appreciate it. doug On 04/02/2015 01:40 AM, A-reum Min wrote: hi doug recon is still not working... if i type the recon-all -i /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071579.dcm -i /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071580.dcm -all -s subj001 then error occured ++ ERROR: GetDICOMInfo(): dcmGetDWIParams() 7 DICOM File: /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071580.dcm ERROR: GetDICOMInfo(): dcmGetDWIParams() 7 DICOM File: /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071581.dcm ERROR: GetDICOMInfo(): dcmGetDWIParams() 7 DICOM File: /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071582.dcm ERROR: GetDICOMInfo(): dcmGetDWIParams() 7 DICOM File: /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071583.dcm ERROR: GetDICOMInfo(): dcmGetDWIParams() 7 DICOM File: /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071584.dcm ERROR: GetDICOMInfo(): dcmGetDWIParams() 7 DICOM File: /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071585.dcm ERROR: GetDICOMInfo(): dcmGetDWIParams() 7 DICOM File: /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071586.dcm ERROR: GetDICOMInfo(): dcmGetDWIParams() 7 DICOM File: /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071587.dcm ERROR: GetDICOMInfo(): dcmGetDWIParams() 7 DICOM File: /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071588.dcm ERROR: GetDICOMInfo(): dcmGetDWIParams() 7 DICOM File: /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071589.dcm ERROR: GetDICOMInfo(): dcmGetDWIParams() 7 DICOM File: /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071590.dcm ERROR: GetDICOMInfo(): dcmGetDWIParams() 7 DICOM File: /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071591.dcm ERROR: GetDICOMInfo(): dcmGetDWIParams() 7 DICOM File: /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071592.dcm ERROR: GetDICOMInfo(): dcmGetDWIParams() 7 DICOM File: /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071593.dcm ERROR: GetDICOMInfo(): dcmGetDWIParams() 7 DICOM File: /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071594.dcm ERROR: GetDICOMInfo(): dcmGetDWIParams() 7 DICOM File: /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071595.dcm ERROR: GetDICOMInfo(): dcmGetDWIParams() 7 DICOM File: /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071596.dcm ERROR: GetDICOMInfo(): dcmGetDWIParams() 7 DICOM File: /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071597.dcm ERROR: GetDICOMInfo(): dcmGetDWIParams() 7 DICOM File: /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071598.dcm ERROR: GetDICOMInfo(): dcmGetDWIParams() 7 DICOM File: /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071599.dcm ERROR: GetDICOMInfo(): dcmGetDWIParams() 7 DICOM File: /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071600.dcm ERROR: GetDICOMInfo(): dcmGetDWIParams() 7 DICOM File: /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071601.dcm ERROR: GetDICOMInfo(): dcmGetDWIParams() 7 DICOM File: /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071602.dcm ERROR: GetDICOMInfo(): dcmGetDWIParams() 7 DICOM File: /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071603.dcm ERROR: GetDICOMInfo(): dcmGetDWIParams() 7 DICOM File: /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071604.dcm ERROR: GetDICOMInfo(): dcmGetDWIParams() 7 DICOM File: /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071605.dcm ERROR: GetDICOMInfo(): dcmGetDWIParams() 7 DICOM File: /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071606.dcm ERROR: GetDICOMInfo(): dcmGetDWIParams() 7 DICOM File: /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071607.dcm ERROR: GetDICOMInfo(): dcmGetDWIParams() 7 DICOM File: /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071608.dcm ERROR: GetDICOMInfo(): dcmGetDWIParams() 7 DICOM File: /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071609.dcm ERROR: GetDICOMInfo(): dcmGetDWIParams() 7 DICOM File: /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071610.dcm ERROR: GetDICOMInfo(): dcmGetDWIParams() 7 DICOM File: /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071611.dcm ERROR: GetDICOMInfo(): dcmGetDWIParams() 7 DICOM File: /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071612.dcm ERROR: GetDICOMInfo(): dcmGetDWIParams() 7 DICOM File: /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071613.dcm ERROR: GetDICOMInfo(): dcmGetDWIParams() 7 DICOM File: /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071614.dcm ERROR: GetDICOMInfo(): dcmGetDWIParams() 7 DICOM File: /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071615.dcm ERROR: GetDICOMInfo(): dcmGetDWIParams() 7 DICOM File: /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071616.dcm ERROR: GetDICOMInfo(): dcmGetDWIParams() 7 DICOM File:
