Freesurfer

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POST-DOCTORAL FELLOWSHIP IN NEUROIMAGING
by Xiaosong He 21 May '18

21 May '18

External Email - Use Caution POST-DOCTORAL FELLOWSHIP IN NEUROIMAGINGTHOMAS JEFFERSON UNIVERSITY/ SIDNEY KIMMEL MEDICAL COLLEGE, PHILA., PA. The Department of Neurology at Thomas Jefferson University/Jefferson Medical College has an opening for a Two-Year Postdoctoral Research Fellowship in Neuroimaging focusing on both clinical brain mapping and primary cognitive neuroscience investigations. The emphasis in our neuroimaging program is on cognitive and behavioral network organization and plasticity in neurologic disorders such as epilepsy. The lab focuses on the use of advanced network neuroscience measures to understand seizure networks and cognitive reorganization in epilepsy, and has had recent publications in Brian, Neurology, and Epilepsia, with some also prompting complimentary peer reviews. The lab is part of the Jefferson Comprehensive Epilepsy Center, an internationally-known epilepsy surgery program. Presurgical brain mapping studies are undertaken (MRI volumetrics, task-fMRI, resting state functional connectivity, diffusion imaging, neuropsychological assessment, electrophysiology/electrocortical stimulation) as well as post-surgical neuroimaging studies investigating clinical, cognitive, and behavioral outcomes. The pre-surgical brain mapping studies are conducted on a regular basis, utilized in image-guided surgery, and then made available for research. Studies in brain recovery and the cognitive reorganization of language and memory functions are emphasized, utilizing rich multi-modal datasets for the investigation of both cognitive and pathologic (e.g., seizure) networks. Thomas Jefferson University provides a high-level interdisciplinary research environment with grand rounds, seminars, case conferences, and opportunities to collaborate with faculty across departments such as neurosurgery and radiology. Successful applicants must have a strong background in image processing and analysis using programs such as MATLAB, SPM, Freesurfer, and FSL with a strong interest in clinical neuroimaging and cognitive neuroscience. Applicants must have a Ph.D. or MD in neuroscience, biomedical engineering, statistics, neurology, neuropsychology, radiology, or related field. Interested applicants should send a CV and cover letter stating experience and interests, 2-3 peer-reviewed publications. Anticipated start date is 7/1/18, but is flexible. Contact: Joseph I. Tracy, Ph.D., ABPP(CN). Director, Cognitive Neuroscience and Brain Mapping Laboratory, Thomas Jefferson Univ./Sidney Kimmel Medical Coll., Jefferson Hospital for Neuroscience, 901 Walnut Street, Suite #447, Phila., PA 19107, phone:#215-955-4661, e-mail: joseph.tracy(a)jefferson.edu. Thomas Jefferson University and Hospitals is an Equal Opportunity Employer. Jefferson values diversity and encourages applications from women, members of minority groups, LGBTQ individuals, disabled individuals, and veterans.

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Re: [Freesurfer] FS_Fast preproc-sess - bbregister misalignment
by Douglas N. Greve 21 May '18

21 May '18

The problem appears to be that your data are not really T2* weighted in that the intensity of cortex (about 830) is less than that of WM (about 862). Try running preproc-sess with -t1 to indicate to bbregister that your data are t1 weighted. On 05/17/2018 03:57 AM, Patrycja Naumczyk wrote: > > > I did not receive an email previously - it occurred I misspelled your > e-mail address. I uploaded the files again, this time with an email > confirmation so it should be working now. > My apologies, > Patrycja > > 2018-05-17 2:52 GMT+02:00 Douglas Greve <dgreve(a)mgh.harvard.edu > <mailto:dgreve@mgh.harvard.edu>>: > > I did not get it. You should have gotten an email. Can you forward > it to me? > > > On 5/16/18 6:50 AM, Patrycja Naumczyk wrote: >> >> >> >> could please confirm receiving the files I sent the other day? By >> any chance, maybe You had a time to look into them? >> >> Best regards, >> Patrycja >> >> 2018-05-14 20:01 GMT+02:00 Patrycja Naumczyk >> <patrycja.naumczyk(a)gmail.com <mailto:patrycja.naumczyk@gmail.com>>: >> >> OK - the 5.3 or the 6.0 version? >> >> 2018-05-14 20:00 GMT+02:00 Douglas N. Greve >> <dgreve(a)mgh.harvard.edu <mailto:dgreve@mgh.harvard.edu>>: >> >> Can you tar up one of your subjects (fmri and FS >> analysis) and send it >> to me on our file drop below? >> >> >> On 05/14/2018 01:58 PM, Patrycja Naumczyk wrote: >> > >> > >> > Hi Doug, >> > >> > we have v.6.0 on a cluster, so I quickly run one >> subject there (the >> > one, whose files and pictures I attached previously). >> This time the >> > BBR-sum was 0.9476, so slightly better but still bad :( >> > >> > Best regards, >> > Patrycja >> > >> > 2018-05-14 16:56 GMT+02:00 Douglas Greve >> <dgreve(a)mgh.harvard.edu <mailto:dgreve@mgh.harvard.edu> >> > <mailto:dgreve@mgh.harvard.edu >> <mailto:dgreve@mgh.harvard.edu>>>: >> > >> > It might be the initialization with FLIRT. Do you >> have access to >> > FS6.0? If so, can you try running 6.0 instead to >> see if it fixes >> > the problem? >> > >> > >> > On 5/14/18 4:05 AM, Patrycja Naumczyk wrote: >> >> >> >> >> >> Hi All, >> >> >> >> I'm still struggling with the registration - so >> far I tried >> >> performing slice-timing and/or motion correction >> in SPM instead >> >> of FS, but that did not changed the results. >> >> >> >> I came up with a new idea, but don't know how to >> verify it. I >> >> used GE scanner for data acquisition, which meant >> I had to >> >> convert the fMRI data and make the directory tree >> myself (as the >> >> dcm-unpack did not work well). I used MRIconvert >> for converting >> >> to nifti, which does not preserve some of the >> FS-Fast crucial >> >> data (i.e. the TR, which I had to update with >> mri_convert in all >> >> files). Is it possible that this is the reason of >> bbregister's >> >> misalignment? Like, the script needs some >> additional information >> >> that should be embedded in the data and is not >> (due to outside >> >> conversion)? >> >> >> >> I was thinking of maybe working around the problem >> by manually >> >> registering the rs-fMRI template to task-based >> template and then >> >> merging the two registration files >> (rs-fMRI_to_taskBased and >> >> taskBased_to_anatomical) and feeding that to the >> preproc-sess >> >> with "-regfile" flag. Potentially it could work, >> but maybe there >> >> is a simpler solution? >> >> >> >> The only difference between the properly aligned >> task-based fMRI >> >> and faulty rs-fMRI is that the latter has lower >> resolution (task >> >> based: 2.5x2.5x3.2mm, rs-fMRI: 3.4x3.4x3.3mm) and >> was longer >> >> (task-based: 160 volumes, rs-fMRI: 400 volumes). >> >> I attach screenshot of the problem in tkregister. >> Left - >> >> task-based fMRI, middle - rs-fMRI, right - rs-fMRI >> with >> >> task-based registration file used. >> >> >> >> Best regards, >> >> Patrycja >> >> >> >> 2018-05-12 15:20 GMT+02:00 Patrycja Naumczyk >> >> <patrycja.naumczyk(a)gmail.com >> <mailto:patrycja.naumczyk@gmail.com> >> <mailto:patrycja.naumczyk@gmail.com >> <mailto:patrycja.naumczyk@gmail.com>>>: >> >> >> >> Hi All, >> >> >> >> I'm running FS v. 5.3 on Gentoo Linux. >> >> >> >> I made a study, where all subjects during one >> session had T1, >> >> resting-state and task-based fMRI. I processed >> all anatomical >> >> data through standard recon-all (it worked >> well), and the >> >> task-based fMRI through FS-FAST - which also >> generated fine >> >> results. >> >> >> >> Now I wanted to look into the rs-fMRI with >> functional >> >> connectivity. I made a separate directory tree >> for this >> >> purpose (in order not to mess task and rest >> data), and >> >> unfortunately the bbregister doesn't handle >> the registration >> >> during preproc-sess properly. Misalignment is >> big and covers >> >> all runs. BBR-sums of all of participants >> (N=39) exceed 0.8 >> >> (some of them exceed 1.0). What's interesting >> is that >> >> bbregister previously managed the task-based >> fMRI data well >> >> (with no BBR-sum exceeding 0.8). I double >> checked the data >> >> for any i.e. conversion/orientation faults, >> but found none. >> >> >> >> The command for preprocessing was identical in >> rs-fMRI and >> >> task-based fMRI: >> >> preproc-sess -sf <sessid> -d >> <ProjectDirectory> -surface >> >> fsaverage lhrh -mni305 -fwhm 5 -per-run -fsd bold >> >> >> >> I attach exemplary register log file from >> rs-fMRI subject >> >> registration (BBRsum=0.9704). This subject's >> task-based fMRI >> >> BBR-sum was 0.55. >> >> >> >> My question is - what may be the cause of such >> a discrepancy >> >> between registration of two functional runs >> taken one by one >> >> (the rs-fMRI preceded the task based)? Does >> anyone have an >> >> idea how to fix the problem? >> >> >> >> Best regards, >> >> Patrycja >> >> >> >> >> >> >> >> >> >> _______________________________________________ >> >> Freesurfer mailing list >> >> Freesurfer(a)nmr.mgh.harvard.edu >> <mailto:Freesurfer@nmr.mgh.harvard.edu> >> >> <mailto:Freesurfer@nmr.mgh.harvard.edu >> <mailto:Freesurfer@nmr.mgh.harvard.edu>> >> >> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> >> >> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> >> > >> > >> > _______________________________________________ >> > Freesurfer mailing list >> > Freesurfer(a)nmr.mgh.harvard.edu >> <mailto:Freesurfer@nmr.mgh.harvard.edu> >> <mailto:Freesurfer@nmr.mgh.harvard.edu >> <mailto:Freesurfer@nmr.mgh.harvard.edu>> >> > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> >> > >> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> <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 >> <http://www.partners.org/complianceline> >> > <http://www.partners.org/complianceline >> <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 mailing list >> > Freesurfer(a)nmr.mgh.harvard.edu >> <mailto:Freesurfer@nmr.mgh.harvard.edu> >> > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> <mailto:Freesurfer@nmr.mgh.harvard.edu> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> >> >> >> >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> <mailto:Freesurfer@nmr.mgh.harvard.edu> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > >

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Re: [Freesurfer] recon-all error: mri_label2label.bin: could not open label file lh.BA1_exvivo.label
by Antonin Skoch 21 May '18

21 May '18

External Email - Use Caution Hi Naomi, does the symbolic link /panfs/pan.fsl.byu.edu/scr/usr/74/intj5/analyses/ACAP-BRAVOS/freesurfer/fsaverage exist in your filesystem? Antonin Skoch Hello FreeSurfer Developers, I'm attempting to run FreeSurfer but I get the following error when I run the recon-all command: > ERROR reading /panfs/pan.fsl.byu.edu/scr/usr/74/intj5/analyses/ACAP-BRAVOS/freesurfer/fsaverage/label/lh.BA1_exvivo.label <" target="_blank" id="ext-gen1283" style="box-sizing: border-box;">http://pan.fsl.byu.edu/scr/usr/74/intj5/analyses/ACAP-BRAVOS/freesurfer/fsa…>; I've searched the list and no similar errors have been reported. Does anyone have any thoughts on how to trouble-shoot this one? Also, Ive attached the recon-all.log in case it's of any use. 1) FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c 2) Platform: Red Hat Enterprise Linux Server release 6.6 (Santiago) 3) uname -a: Linux m8-8-5 2.6.32-696.18.7.el6.x86_64 #1 SMP Thu Dec 28 20:15:47 EST 2017 x86_64 x86_64 x86_64 GNU/Linux 4) recon-all.log: see attached Thanks, Naomi

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recon-all error: mri_label2label.bin: could not open label file lh.BA1_exvivo.label
by Naomi Hunsaker 21 May '18

21 May '18

External Email - Use Caution Hello FreeSurfer Developers, I'm attempting to run FreeSurfer but I get the following error when I run the recon-all command: > ERROR reading /panfs/pan.fsl.byu.edu/scr/usr/74/intj5/analyses/ACAP-BRAVOS/freesurfer/fsaverage/label/lh.BA1_exvivo.label <http://pan.fsl.byu.edu/scr/usr/74/intj5/analyses/ACAP-BRAVOS/freesurfer/fsa…> I've searched the list and no similar errors have been reported. Does anyone have any thoughts on how to trouble-shoot this one? Also, Ive attached the recon-all.log in case it's of any use. 1) FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c 2) Platform: Red Hat Enterprise Linux Server release 6.6 (Santiago) 3) uname -a: Linux m8-8-5 2.6.32-696.18.7.el6.x86_64 #1 SMP Thu Dec 28 20:15:47 EST 2017 x86_64 x86_64 x86_64 GNU/Linux 4) recon-all.log: see attached Thanks, Naomi Naomi J. Goodrich-Hunsaker, Ph.D. Research Associate University of Utah e. naomi.hunsaker(a)utah.edu <mailto:naomi.hunsaker@utah.edu> w. http://biabl.github.io <https://esig.ly/links/255317> Follow me: <https://esig.ly/links/255318> <https://esig.ly/links/255319> <https://esig.ly/links/255320> <https://esig.ly/links/255321> <https://esig.ly/links/255322> <https://esig.ly/links/255323> <https://esig.ly/links/255324>

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Error results mris_make_surfaces
by Pam Garcia 21 May '18

21 May '18

External Email - Use Caution Hello, experts I have a problem with the results of mris_make_surfaces to pial and white matter surfaces. I am working with high resolution (0.75x0.75x0.75) monkey images, mris_makes_surfaces finish without errors but the surfaces have notches, I attach an image as an example of the error. This is the line that I am using mris_make_surfaces -whiteonly -noaparc -noaseg -mgz -T1 brain.finalsurfs subject lh. The error only appers with mris_make_surfaces, the segmentation of wm and ?h.orig looks good. Thanks a lot Pam [image: Screenshot from 2018-05-18 14:29:12.png]

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mris_fwhm
by Eduard Vilaplana Martinez 21 May '18

21 May '18

External Email - Use Caution Dear freesurfer experts, I would like to ask you about the mris_fwhm script. What does the flag "--mask" exactly do? Suppose I would like to compute the effective smoothness of an mri dataset. Some subjects have zeros in some vertices, but instead of using the prune option, I would like to use all the available signal, so I have to use a different mask for every subject. Would the option mask do the job in that case and would accept the multidimensional mask? Or rather the "--mask" option expects for a single (not multidimensional) mask? Any insight would be greatly appreciated. Thanks in advance, Eduard Vilaplana. Unitat de Memòria/Memory Unit Servei de Neurologia/Neurology Department Hospital de la Santa Creu i Sant Pau Sant Antoni Mª Claret 167 Barcelona 08025 Spain (Tel) +34 93 556 59 86 (ext 8229) Email:evilaplana@santpau.cat http://santpaumemoryunit.com/

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Inquiry about error when run "-local GI"
by subin oh 21 May '18

21 May '18

External Email - Use Caution Hello, FreeSurfer Developers. I run "recon-all -s test01_t1 -local GI" for my subject after the MATLAB path (%PATH = “/Applications/MATLAB_R2014b.app/bin”:”$PATH”) The original Setting of the FreeSurfer(Mac OS) is like this : But it exited with errors as follows: I guess Outer ROI or matrix...but I couldn't know what the problem exactly is.. Improper assignment with rectangular empty matrix. > > Error in dsearchn (line 79) > [d(i),t(i)] = min(sum((x-yi).^2,2)); > Error in mesh_vertex_nearest (line 29) > nearestIndex = dsearchn(vertices,points); > > Error in reorganize_verticeslist (line 28) > [nextindex,nextvalue]=mesh_vertex_nearest(mesh_total.vertice > s(remaininglist,:),mesh_total.vertices(verticeslist(start_vertex),:)); > > Error in make_roi_paths (line 93) > reorglist = reorganize_verticeslist (mesh_total, A, mesh_outer, perim, > verticeslist, step); > > >> > ERROR: make_roi_paths did not complete successfully! > Darwin Chans-iMac.local 13.4.0 Darwin Kernel Version 13.4.0: Mon Jan 11 > 18:17:34 PST 2016; root:xnu-2422.115.15~1/RELEASE_X86_64 x86_64 > recon-all -s test01_t1 exited with ERRORS at Mon May 21 09:50:03 KST 2018 > For more details, see the log file /Applications/freesurfer/subje > cts/test01_t1/test01_t1/scripts/recon-all.log > To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/ > BugReporting I attached two relevant MATLAB files (*make_roi_pattern.m, SearchProjectionOnPial_Ver2.m*) and all the error message are written below.. Could you tell me some advice? Best regards, Subin Oh -------- [freesurfer-Darwin-lion-stable-pub-v5.3.0]------------------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /Applications/freesurfer FSFAST_HOME /Applications/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /Applications/freesurfer/subjects MNI_DIR /Applications/freesurfer/mni FSL_DIR /usr/local/fsl ----------------------------------------------------------------------------------------------------------------------------------------- Chans-iMac:subjects roh$ PATH="/Applications/MATLAB_R2014b.app/bin":"$PATH" Chans-iMac:subjects roh$ recon-all -s test01_t1 -localGI Subject Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0 Current Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0 INFO: SUBJECTS_DIR is /Applications/freesurfer/subjects/test01_t1 Actual FREESURFER_HOME /Applications/freesurfer -rw-rw-r-- 1 roh staff 484107 May 18 17:36 /Applications/freesurfer/subje cts/test01_t1/test01_t1/scripts/recon-all.log Darwin Chans-iMac.local 13.4.0 Darwin Kernel Version 13.4.0: Mon Jan 11 18:17:34 PST 2016; root:xnu-2422.115.15~1/RELEASE_X86_64 x86_64 /Applications/freesurfer/subjects/test01_t1/test01_t1/surf #-------------------------------------------- #@# Local Gyrification Index lh Mon May 21 09:47:51 KST 2018 \n mris_compute_lgi --i lh.pial \n ================= rm -Rf /Applications/freesurfer/subjects/test01_t1/test01_t1/surf/ tmp-mris_compute_lgi-lh.pial ================= ================= mkdir -p /Applications/freesurfer/subjects/test01_t1/test01_t1/surf/ tmp-mris_compute_lgi-lh.pial ================= ================= mris_fill -c -r 1 lh.pial /Applications/freesurfer/subje cts/test01_t1/test01_t1/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz ================= reading surface from lh.pial... writing filled volume to /Applications/freesurfer/subje cts/test01_t1/test01_t1/surf/tmp-mris_compute_lgi-lh.pial/ lh.pial.filled.mgz... conforming output volume setting resolution for intermediate calculations to 1.0000 ================= make_outer_surface('/Applications/freesurfer/subjects/ test01_t1/test01_t1/surf/tmp-mris_compute_lgi-lh.pial/lh. pial.filled.mgz',15,'/Applications/freesurfer/subjects/ test01_t1/test01_t1/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer'); exit ================= < M A T L A B (R) > Copyright 1984-2014 The MathWorks, Inc. R2014b (8.4.0.150421) 64-bit (maci64) September 15, 2014 For online documentation, see http://www.mathworks.com/support For product information, visit www.mathworks.com. >> reading filled volume... closing volume... morphological closing done. writing outer surface... ================= mris_extract_main_component /Applications/freesurfer/subje cts/test01_t1/test01_t1/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer /Applications/freesurfer/subjects/test01_t1/test01_t1/surf/ tmp-mris_compute_lgi-lh.pial/lh.pial-outer-main ================= counting number of connected components... 59754 voxel in cpt #1: X=2 [v=59754,e=179256,f=119504] located at (-26.107368, -18.544823, 16.176725) For the whole surface: X=2 [v=59754,e=179256,f=119504] One single component has been found nothing to do done ================= mris_smooth -nw -n 30 /Applications/freesurfer/subje cts/test01_t1/test01_t1/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer-main ./lh.pial-outer-smoothed ================= smoothing for 30 iterations smoothing surface tessellation for 30 iterations... smoothing complete - recomputing first and second fundamental forms... ================= mris_euler_number ./lh.pial-outer-smoothed ================= euler # = v-e+f = 2g-2: 59754 - 179256 + 119504 = 2 --> 0 holes F =2V-4: 119504 = 119508-4 (0) 2E=3F: 358512 = 358512 (0) total defect index = 0 ================= mris_convert -n lh.pial-outer-smoothed /Applications/freesurfer/subje cts/test01_t1/test01_t1/surf/tmp-mris_compute_lgi-lh.pial/ lh.pial-outer-smoothed-normals.asc ================= ================= find_corresponding_center_FSformat('lh.pial','lh.pial-outer- smoothed',100,'/Applications/freesurfer/subjects/test01_t1/ test01_t1/surf/tmp-mris_compute_lgi-lh.pial','/tmp/mrc_46281_.m'); exit ================= < M A T L A B (R) > Copyright 1984-2014 The MathWorks, Inc. R2014b (8.4.0.150421) 64-bit (maci64) September 15, 2014 For online documentation, see http://www.mathworks.com/support For product information, visit www.mathworks.com. >> FREESURFER_READ_SURF [v 1.2 ] ...reading surface file: lh.pial ...reading triangle file ...adding 1 to face indices for matlab compatibility. ...done ( 0.08 sec) FREESURFER_READ_SURF [v 1.2 ] ...reading surface file: lh.pial-outer-smoothed ...reading triangle file ...adding 1 to face indices for matlab compatibility. ...done ( 0.01 sec) deltaT = 2.5700 ================= make_roi_paths('lh.pial','lh.pial-outer-smoothed',25,100,'/A pplications/freesurfer/subjects/test01_t1/test01_t1/surf/ tmp-mris_compute_lgi-lh.pial','/tmp/mrp_46281_.m'); exit ================= < M A T L A B (R) > Copyright 1984-2014 The MathWorks, Inc. R2014b (8.4.0.150421) 64-bit (maci64) September 15, 2014 For online documentation, see http://www.mathworks.com/support For product information, visit www.mathworks.com. >> loading datas ... FREESURFER_READ_SURF [v 1.2 ] ...reading surface file: lh.pial ...reading triangle file ...adding 1 to face indices for matlab compatibility. ...done ( 0.08 sec) FREESURFER_READ_SURF [v 1.2 ] ...reading surface file: lh.pial-outer-smoothed ...reading triangle file ...adding 1 to face indices for matlab compatibility. ...done ( 0.01 sec) preparing outer mesh structure ... face 5000 / 119504 face 10000 / 119504 face 15000 / 119504 face 20000 / 119504 face 25000 / 119504 face 30000 / 119504 face 35000 / 119504 face 40000 / 119504 face 45000 / 119504 face 50000 / 119504 face 55000 / 119504 face 60000 / 119504 face 65000 / 119504 face 70000 / 119504 face 75000 / 119504 face 80000 / 119504 face 85000 / 119504 face 90000 / 119504 face 95000 / 119504 face 100000 / 119504 face 105000 / 119504 face 110000 / 119504 face 115000 / 119504 mesh_outer = vertices: [59754x3 double] faces: [119504x3 double] facesOfVertex: [59754x1 struct] preparing pial mesh structure ... ...searching for mesh edges...done (76.35 sec). ... creating path file for vertex 1 / 59754 area file for outer ROIs saved at 1 Improper assignment with rectangular empty matrix. 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.vertice s(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! Darwin Chans-iMac.local 13.4.0 Darwin Kernel Version 13.4.0: Mon Jan 11 18:17:34 PST 2016; root:xnu-2422.115.15~1/RELEASE_X86_64 x86_64 recon-all -s test01_t1 exited with ERRORS at Mon May 21 09:50:03 KST 2018 For more details, see the log file /Applications/freesurfer/subje cts/test01_t1/test01_t1/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/ BugReporting

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Definition of anatomical features
by SJ JV 18 May '18

18 May '18

External Email - Use Caution Hi Can someone please give the definitions for the following anatomical features obtained from freesurger aseg.stats ? Are they thickness or area or volume measures ? - anatomy_Left-Lateral-Ventricle - anatomy_Left-Inf-Lat-Vent - anatomy_Left-Cerebellum-White-Matter - anatomy_Left-Cerebellum-Cortex - anatomy_Left-Thalamus-Proper - anatomy_Left-Caudate - anatomy_Left-Putamen - anatomy_Left-Pallidum - anatomy_3rd-Ventricle - anatomy_4th-Ventricle - anatomy_Brain-Stem - anatomy_Left-Hippocampus - anatomy_Left-Amygdala - anatomy_CSF - anatomy_Left-Lateral-Ventricle - anatomy_Left-Inf-Lat-Vent - anatomy_Left-Cerebellum-White-Matter - anatomy_Left-Cerebellum-Cortex - anatomy_Left-Thalamus-Proper - anatomy_Left-Caudate - anatomy_Left-Putamen - anatomy_Left-Pallidum - anatomy_3rd-Ventricle - anatomy_4th-Ventricle - anatomy_Brain-Stem - anatomy_Left-Hippocampus - anatomy_Left-Amygdala - anatomy_CSF - anatomy_Left-VentralDC - anatomy_Left-vessel - anatomy_Left-choroid-plexus - anatomy_Right-Lateral-Ventricle - anatomy_Right-Inf-Lat-Vent - anatomy_Right-Cerebellum-White-Matter - anatomy_Right-Cerebellum-Cortex - anatomy_Right-Thalamus-Proper - anatomy_Right-Caudate - anatomy_Right-Putamen - anatomy_Right-Pallidum - anatomy_Right-Hippocampus - anatomy_Right-Amygdala - anatomy_Right-VentralDC - anatomy_Right-vessel - anatomy_Right-choroid-plexus - anatomy_5th-Ventricle - anatomy_WM-hypointensities - anatomy_Left-WM-hypointensities - anatomy_Right-WM-hypointensities - anatomy_non-WM-hypointensities - anatomy_Left-non-WM-hypointensities - anatomy_Right-non-WM-hypointensities - anatomy_Optic-Chiasm - anatomy_CC_Posterior - anatomy_CC_Mid_Posterior - anatomy_CC_Central - anatomy_CC_Mid_Anterior - anatomy_CC_Anterior Thanks S.V -- U

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gcs and gca to coordinates
by Tim Hahn 18 May '18

18 May '18

External Email - Use Caution Dear all, thanks for building and maintaining freesurfer. It's really a great tool. My question is very simple: I have three Freesurfer Atlas files (lh and rh curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs and RB_all_2008-03-26.gca) and would like to either get all coordinates in a given area and/or a nifti/img. I realize that the gcs and gca files contain much more information. However, I just need the location information and ROI name for a meta-analytic approach based on the literature. Is there any way to get this information? Thanks a lot! Cheers, Tim

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LGI trouble with Matlab
by subin oh 18 May '18

18 May '18

External Email - Use Caution Hello, I downloaded the Freesurfer ver 5.3.0 and installed it on Mac OS. I run *"recon-all -s <subject> -local GI" *for my subject.. And I run *Matlab Script* about "*Start up" , "make_outer_surface", "make_roi_paths" , "find correspoding center" *as follows: But it exited with same *errors* as follows: Please Could you tell me the way for correcting that error and to calculate the LGI? *the error message is..* Thank you very much. Best Regards, Subin =====================[Mac OS Error]====================== -------- freesurfer-Darwin-lion-stable-pub-v5.3.0 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /Applications/freesurfer FSFAST_HOME /Applications/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /Applications/freesurfer/subjects MNI_DIR /Applications/freesurfer/mni FSL_DIR /usr/local/fsl Chans-iMac:subjects roh$ recon-all -s test01_t1 -localGI Subject Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0 Current Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0 INFO: SUBJECTS_DIR is /Applications/freesurfer/subjects/test01_t1 Actual FREESURFER_HOME /Applications/freesurfer -rw-rw-r-- 1 roh staff 468188 May 18 16:01 /Applications/freesurfer/subjects/test01_t1/test01_t1/scripts/recon-all.log Darwin Chans-iMac.local 13.4.0 Darwin Kernel Version 13.4.0: Mon Jan 11 18:17:34 PST 2016; root:xnu-2422.115.15~1/RELEASE_X86_64 x86_64 /Applications/freesurfer/subjects/test01_t1/test01_t1/surf #-------------------------------------------- #@# Local Gyrification Index lh Fri May 18 17:36:00 KST 2018 \n mris_compute_lgi --i lh.pial \n ERROR: Matlab is required to run mris_compute_lgi! Darwin Chans-iMac.local 13.4.0 Darwin Kernel Version 13.4.0: Mon Jan 11 18:17:34 PST 2016; root:xnu-2422.115.15~1/RELEASE_X86_64 x86_64 recon-all -s test01_t1 exited with ERRORS at Fri May 18 17:36:00 KST 2018 For more details, see the log file /Applications/freesurfer/subjects/test01_t1/test01_t1/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting =============================================================== *the Matlab Scripts are..* =================[Matlab Script: StartUp]====================== % freesurfer start fshome = getenv('FREESURFER_HOME'); fsmatlab = sprintf('%s/matlab',fshome); if (exist(fsmatlab) == 7) path(path,fsmatlab); end clear fshome fsmatlab; =================[Matlab Script: make_outer_surface]================ function make_outer_surface (filled_volume, se_diameter, output_surface) % Original Author: Marie Schaer % Date: 2007/11/14 % % This function takes as an input the binary volume resulting of the % filling of the any surface (usually the pial one) using mris_fill, and % will close the sulci using morphological operation, with a sphere as the % structural element. % % Parameters: % se_diameter is the diameter of the sphere (in mm), use 15mm by default % to close the sulci. % % Utilities to write the surface to the freesurfer format are modified from % "freesurfer_write_surf" (from Darren Weber's bioelectromagnetism toolbox), % according to a suggestion by Don Hagler in FreeSurfer's mailing list on % August 3, 2007. % % Example: make_outer_surface('lh.pial.mgz',15,'lh.outer-pial') fprintf('reading filled volume...\n'); vol=MRIread(filled_volume); volume=vol.vol; volume(volume==1)=255; fprintf('closing volume...\n'); % first apply a very soft gaussian filter, with sigma = 1mm, in order to % facilitate the closing Gaussian = fspecial('gaussian',[2 2],1); image_f=zeros(256,256,256); for slice=1:256 temp = double(reshape(volume(:,:,slice),256,256)); image_f(:,:,slice) = conv2(temp,Gaussian,'same'); end image2=zeros(size(image_f)); image2(image_f<=25)=0; image2(image_f>25)=255; se=strel('ball',se_diameter,se_diameter); BW2=imclose(image2,se); thresh = max(BW2(:))/2; i=find(BW2<=thresh); BW2(i)=0; i=find(BW2>thresh); BW2(i)=255; [f,v] = isosurface(BW2,100); v2=[129-v(:,1) v(:,3)-129 129-v(:,2)]; % in order to cope with the different orientation v=v2; fprintf('morphological closing done.\n'); fprintf('writing outer surface...\n'); fname=output_surface; vert = v; face = f - 1; vnum = size(vert,1); fnum = size(face,1); % open it as a big-endian file fid = fopen(fname, 'wb', 'b'); TRIANGLE_FILE_MAGIC_NUMBER = 16777214; fwrite3(fid, TRIANGLE_FILE_MAGIC_NUMBER); % Ouput a couple of text lines with creation date str = sprintf('created from matlab on %s\n',datestr(now)); fwrite(fid, str,'char'); fwrite(fid, vnum,'int32'); fwrite(fid, fnum,'int32'); % reshape vert into column array and write vert = reshape(vert',size(vert,1)*size(vert,2),1); fwrite(fid, vert,'float32'); % reshape face into column array and write face = reshape(face',size(face,1)*size(face,2),1); fwrite(fid, face,'int32'); fclose(fid) ; return end =================[Matlab Script: make_roi_paths]=============== function make_roi_paths(pial, outersmoothed, radius, stepsize, outdir, flagf) % Original Author: Marie Schaer % Date: 2007/11/15 % % This function creates multiple circular regions of interest on the outer % surface, measures their area (saved in matlab format) and save path file % containing a set of % corresponding points on the pial surface. The path files are required as % an input to the mri_path2label function % % Parameters: % radius: radius of the circular region of interest on the outer surface. % Most appropriate values between 20 and 25 mm, further documentation % available in the validation publication: "A surface-based approach to % quantify local cortical gyrification" by Schaer M, Bach Cuadra M, % Tamarit L, Eliez E, Thiran JP, IEEE Transactions on Medical Imaging, 2007 % % Utilities to transfer points on the pial surface calls "mesh_vertex_nearest", % a function written by Darren Weber. Utilities to compute matrix adjacency % for the pial surface calls "mesh_adjacency", a program first written by % Darren Weber, then modified by G. Peyre (source: toolbox_graph on % mathworks) % % Example: make_roi_paths('lh.pial','lh.outer-pial-smoothed',25,100,/tmp) t0 = cputime; disp('loading datas ...') [mesh_total.vertices, mesh_total.faces]=freesurfer_read_surf(pial); [mesh_outer.vertices, mesh_outer.faces]=freesurfer_read_surf(outersmoothed); disp('preparing outer mesh structure ...') mesh_outer = createMeshFacesOfVertex (mesh_outer.vertices, mesh_outer.faces) disp('preparing pial mesh structure ...') A = mesh_adjacency(mesh_total); % Keep track of the area for each individual region of interest on the % outer surface: nbVertices = size(mesh_outer.vertices,1); areasOuterROI = zeros(nbVertices,1); areasOuterROI = sparse (areasOuterROI); clear nbVertices % Circular regions of interest are defined each 100 vertex on the outer % surface. Due to the high resolution of the outer mesh (average face area % of ~0.3mm2), calculations are computed each 1 on 100 vertex, to avoid % high redundancies and optimize calculation time. for iV = 1:stepsize: length(mesh_outer.vertices) disp(['... creating path file for vertex ',num2str(iV),' / ' ,num2str(length(mesh_outer.vertices))]) % ------ Part 1: find the ROI on the enveloppe -------------- [verticesInROI, facesInROI] = getVerticesAndFacesInSphere(mesh_outer, iV, radius); % In rare case, the intersection of the enveloppe with the sphere result % in two regions of interest: the one that we expect, circular and % centered in iV; and an aberrant one at the bottom of the sphere % (e.g. near the superior sagittal vault). The next step is used to % control for that and keep only the radial region centered at iV. facesListOuterGeo = MakeGeodesicOuterROI (mesh_outer, iV, facesInROI); % Find the perimeter of the outer ROI verticesOuterGeo=unique(facesListOuterGeo(:)); perim=setdiff(verticesOuterGeo,verticesInROI); % Measure its area areaOuterROI = getFacesArea(mesh_outer,facesListOuterGeo); areasOuterROI(iV) = areaOuterROI; if (mod(iV,50*stepsize) == 1) fname = [outdir '/' pial '.area_intermed.mat']; save(fname, 'areasOuterROI') ; disp(['area file for outer ROIs saved at ',num2str(iV)]) end clear verticesInROI facesInROI facesListOuterGeo verticesOuterGeo areaOuterROI % ----- Part2: Define the corresponding set of points on the pial surface: % Transfer a few points of the perimeter of the hulls ROI from % the envelope to the pial surface, and save them as path file. step = 7; [verticeslist] = SearchProjectionOnPial(mesh_total, mesh_outer, perim, step); % reorganize the set of points in the right order to input them to % mri_path2label reorglist = reorganize_verticeslist (mesh_total, A, mesh_outer, perim, verticeslist, step); lindex = reorglist'; lxyz = mesh_total.vertices(lindex,:); lindex= lindex-1; p = sprintf ('%06d', iV); write_path(lxyz, lindex,[outdir '/' pial '.' p '.path']); clear verticeslist lindex lxyz end disp(['saving area file in matlab format... ']) fname = [outdir '/' pial '.outer_ROIs_area.mat']; save(fname, 'areasOuterROI') disp('DONE.') deltaT = cputime - t0 % indicate successful completion by deleting flagfile delete(flagf); =======================[find corresponding_center_FSformat]========================= t0 = cputime; [mesh_pial.vertices, mesh_pial.faces] = freesurfer_read_surf(pial); [mesh_outer.vertices, mesh_outer.faces] = freesurfer_read_surf(outersmoothed); fidv = fopen([outdir '/' pial '.center.vertices'], 'w') ; for iV = 1 :stepsize: length(mesh_outer.vertices) centerSeed=mesh_vertex_nearest(mesh_pial.vertices,mesh_outer.vertices(iV,:)); centerSeed = centerSeed - 1; %FreeSurfer-s vertex are 0-based p = sprintf ('%06d', iV); fid = fopen([outdir '/' pial '.' p '.center'], 'w') ; fprintf(fid,'%d\n',centerSeed); fclose(fid) ; fprintf(fidv,'%s\n',p); end fclose(fidv) ; deltaT = cputime - t0 % indicate successful completion by deleting flagfile delete(flagfile); ===================================================================================

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