Freesurfer

freesurfer@nmr.mgh.harvard.edu

14 participants
30083 discussions

white matter edits not incorporated
by dgw 21 Apr '16

21 Apr '16

Hi, I recently edited a brain with a gyral cyst, carefully filling the cyst with white matter in the wm.mgz. Unfortunately after running: /usr/local/freesurfer/stable5_3_0/bin/recon-all -autorecon2-wm -autorecon3 -subjid nmr01002 -FLAIRpial -openmp 8 none of the edits were incorporated. Is the FLAIRpial flag incompatible with autorecon2-wm? Is there some other misake? I followed this guide https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/WhiteMatterEdits_freev… Thanks, Dan

3 11

Qdec interface issue
by Sahil Bajaj 21 Apr '16

21 Apr '16

Hello, I am working on measuring cortical thickness of a patient group. I am using Ubuntu 14.04 Somehow, if I use command line to perform the analysis, Freesurfer/qdec is working fine but if I use Qdec interface, it works fine initially but when I switch to display window, it doesn't allow me to change/edit FDR p-values, threshold min and max, although I can click on all the options on display window e.g. inflated, pial, white, etc. Also, when I tried to do the same on other computer (Mac), it works fine for me. I was wondering if this is because of video card problem or something. The thing is it was working before for some time, then after a computer crash, it no longer works. We replaced the video card but are still experiencing the same problem. At this point I would welcome any suggestions. Thanks, Sahil -- -- ------------------------------------------------- Sahil Bajaj Post-doctoral Fellow Nantz National Alzheimer's Center, Department of Neurology The Houston Methodist Research Institute (THMRI) Houston, TX, USA. E-mail:sahil.brain@gmail.com <E-mail%3Asahil.phy(a)gmail.com>

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"Bump" - Fwd: lGI value is aberrantly high and misalignment fix
by Marco Bucci 21 Apr '16

21 Apr '16

I forward again my email, that has not been sent to the mailing list yet. ---------- Forwarded message ---------- From: Marco Bucci <bucci.marco(a)gmail.com> Date: 2016-03-22 10:05 GMT+02:00 Subject: Re: [Freesurfer] "Bump" - Fwd: lGI value is aberrantly high and misalignment fix To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Dear Marie and Freesurfer Users, thanks for your support. I could not imagine that freeview was visualizing wrongly the surfaces. For this reason, my colleague and I have added a small "integrity check" with which we compare the min and max of the vertexes coordinates of pial and pial-outer. If the pial min and max are closer to the center it means that pail is included in the outer surface. We believe this is faster than checking visually with the viewer all the surfaces, slice by slice. The subject surfaces of which I sent you the recon.log passed the test. But... I ran another case and unfortunately it did not pass the check. I attach the recon log, the screenshot of tkmedit with lh.pial going below the outer surface. Is it important for the lgI calculation purposes? I also attach the Matlab code for the testing (it is rough, but works) It is possible to check with a stepsize of 1 to be absolutely sure about any intersection, but it takes longer time. Looking forward to hear from you soon. Thanks in advance for your help Yours, Marco (and Harri) P.S. I went back to the original line 51 of the Marie Schaer code in "make_outer_surface". No "fix" anymore. 2016-03-17 23:19 GMT+02:00 Marie Schaer <Marie.Schaer(a)unige.ch>: > > Hi Marco, > > It’s pretty strange because from the recon-all.log you sent, the first LGI > process went fine (line 14584 and 19329 for the right and left hemispheres, > on Dec 15). Then you don’t run anything else on the surfaces and just > reprocess the exact same LGI process for the same subject (Dec 18), and you > get different values from what you just had, with many values <1, plus it > gets stuck. > > Could that be related to your change on line 51 in make_outer_surface? > When you say misalignment, do you mean in freeview or tkmedit? Because we > saw some occurrences of misalignment in freeview, which indeed are related > to the surface format and as long as the surfaces align well in tkmedit > then you should definitely not change anything in the make_outer_surface > code. > > Keep me posted, > > Marie > > > On 16 Mar 2016, at 02:51, Marco Bucci <bucci.marco(a)gmail.com> wrote: > > Dear all, > > I forward again my original post. > I also attach the recon-all.log of one of the several faulty cases. > > I run freesurfer (freesurfer-Darwin-lion-stable-pub-v5.3.0) > in Mac OS X 10.9.4 and -lgI option with Matlab_R2013a > and I have fixed the SearchProjectionOnPial.m. > > I also had to fix line 51 of make_outer_surface.m > "v2=[129-v(:,1) v(:,3)-129 129-v(:,2)]; % in order to cope with the > different orientation" > with > "v2=[vol.vox2ras1(1,4)-v(:,1) v(:,3)+vol.vox2ras1(2,4) > vol.vox2ras1(3,4)-v(:,2)];" > in order to use the image coordinate to fix surface orientation and > alignment. > > If I would use the original line 51, the surface produced by recon -lgi > results > misaligned with the reference pial and image. > > My problems remains the aberrantly high lgI value in most of my subject > images. > > Can you help me? > > Yours, > Marco Bucci > > > ---------- Forwarded message ---------- > From: Marco Bucci <bucci.marco(a)gmail.com> > Date: 2015-12-22 23:49 GMT+02:00 > Subject: Re: [Freesurfer] lGI value is aberrantly high > To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> > > > Dear all, > > I have a problem with the LGI module. > At the step when the software computes the LGIs for the vertices, > In one vertex the lGI results aberrantly high and the software exits > with ERRORS. > > I tried the solution suggested by Marie Schaer to rereconstruct > The images with "randomness" > Recon-all -autorecon2-wm -randomness -autorecon3 > > I tried this fix on two of my subjects > With errors. Not all subject resulted > Errors in the computation of the gyrification. > > Can you help me? > > Marco Bucci > Turku Pet Center > > Sent from my iPhone > > > > -- > **************************************************** > Marco Bucci, PhD in > Clinical Physiology and Nuclear Medicine > Turku PET Centre > Turku University Central Hospital (TUCH) > PL 52, Kiinanmyllynkatu 4-8, 20521 Turku, Finland > tel. +358 2 3132798 > fax. +358 2 2318191 > mobile: +358 40 6873976 > UTU e-mail: marbuc(a)utu.fi > **************************************************** > <recon-all.log>_______________________________________________ > Freesurfer mailing list > Freesurfer(a)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 mailing list > Freesurfer(a)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. > > -- **************************************************** Marco Bucci, PhD in Clinical Physiology and Nuclear Medicine Turku PET Centre Turku University Central Hospital (TUCH) PL 52, Kiinanmyllynkatu 4-8, 20521 Turku, Finland tel. +358 2 3132798 fax. +358 2 2318191 mobile: +358 40 6873976 UTU e-mail: marbuc(a)utu.fi **************************************************** -- **************************************************** Marco Bucci, PhD in Clinical Physiology and Nuclear Medicine Turku PET Centre Turku University Central Hospital (TUCH) PL 52, Kiinanmyllynkatu 4-8, 20521 Turku, Finland tel. +358 2 3132798 fax. +358 2 2318191 mobile: +358 40 6873976 UTU e-mail: marbuc(a)utu.fi ****************************************************

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identity.nofile
by Trisanna Sprung-Much 20 Apr '16

20 Apr '16

Hi All! Could someone please tell me how to run mri_vol2surf using identity.nofile as the transformation? I cannot find any documentation on identity.nofile Additionally, if my next step is to use the output of mri_vol2surf in mri_cor2label, which takes surface overlays OR volumes, what format should my output be for mri_vol2surf? many thanks! Trisanna -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology

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Preprocessing task data with multiple B0-corrected runs
by Shea, Conor 20 Apr '16

20 Apr '16

Dear Doug, I'm trying to use FSFAST to analyze task data with multiple runs. Before using the preproc-sess pipeline, I ran B0 correction on each of the runs, so I have 3 different b0dcmap files. I'm trying to figure out the best way to run preprocessing on the three runs simultaneously using preproc-sess, but I don't know how to get FSFAST to use each run's specific b0dcmap in the preprocessing of each run's data. FSFAST wants the b0dcmap files to be in the task folder, but how can it differentiate between the three b0dcmap files if they're not in the run folders? Thanks, Conor

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Functional Connectivity with Hippocampal Subfields as seeds
by Julio Alberto González Torre 20 Apr '16

20 Apr '16

Hi Freesurfers. As I'm currently performing the Funcional Conectivity workflow with FSFAST, the 4th step requires me to choose the areas to use as seeds. I would like to use the hippocampal subfields as seeds, but I can't select them because the aparc+aseg.mgz doesn't contains those labels. The only area available is the whole hippocampus, which implies a huge seed that doesn't discriminate the subfields, and I'm interested in exploring if there are conectivity differences between the subfields. Is there any way to create the seeds for each subject using the hippocampal subfields as reference? Thanks a lot.

2 1

Lme matlab tools lhstats
by Patrizia Dall'Acqua 20 Apr '16

20 Apr '16

Dear FS-Group I am attempting to use the lme matlab tools for my longitudinal analysis. My dataset consists of 2 time-points and 2 groups (patients and controls). I will not use covariates since the groups are well matched for age, gender and education. I am trying to adapt the wiki instructions of the mass-univariate model to our data. Our design matrix X contains 4 columns: 1. intercept 2. time 3. group 4. interaction group*time Our Cmd history: [Y,mri] = fs_read_Y('lh.thickness_sm15.mgh'); lhsphere = fs_read_surf('/subjects/average_LTHV_long_all_49/surf/lh.sphere'); lhcortex = fs_read_label('/subjects/average_LTHV_long_all_49/label/lh.cortex.label'); Qdec = fReadQdec('qdec.long.table_4columns.txt'); Qdec = rmQdecCol(Qdec,1); sID = Qdec(2:end,1); Qdec = rmQdecCol(Qdec,1); M = Qdec2num(Qdec); [M,Y,ni] = sortData(M,1,Y,sID); X = [ones(length(M),1) M M(:,1).*M(:,2)]; lhstats = lme_mass_fit_vw(X, [4], Y, ni, lhcortex) I am mainly interested in comparing longitudinal changes between groups (group*time interaction) but also interested in the main effect of group and time. I have two questions: 1. I am not sure about my „interpretation“ of random and fixed effect. Since I am interested in the group*time interaction (4. column), does it make sense to use a single random effect for this interaction or should I take a second random effect for time (2. column)? 2. If a model with two random effects make sense (2. and 4. column), should I compare the model including two random effects with a model with a single random effect to test which one is significantly better? Thank you for your help! Patrizia

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how to add skull and scalp and how to convert RAS coordinates
by Chiara Bulgarelli 20 Apr '16

20 Apr '16

Dear FreeSurfer users, I am a PhD student from Birkbeck University and I am trying to segment some structural images of infants data. After the classical segmentation done with the ‘-recon all’ function, I am stuck with two issues: 1. How can I add the CSF, the skull and the scalp in my model? I know that with FS you can get just WM and GM. 2. How can I convert the RAS coordinates to MNI ones? I have been trying to look at these topics on line and on the FreeSurfer website, but I haven’t find anything useful so far. Many thanks in advance for your help! Best Regards Chiara ---------------- Chiara Bulgarelli PhD Student, Centre for Brain and Cognitive Development Birkbeck College, University of London cbulga01(a)mail.bbk.ac.uk // bulgarelli.chiara3(a)gmail.com

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entorhinal & temporal pole thickness measurements
by Mihaela Stefan 20 Apr '16

20 Apr '16

Dear Freesurfers, We noticed that some subjects in our study have the average cortical thickness values in entorhinal and temporal pole above 4 mm. They are adolescent girls so they're pretty young but we wonder if these values are accurate. Visually, their segmentations seem good. In an older email, Bruce was recommending using _exvivo.stats instead of aparc for entorhinal measurements: https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg26364.html Is there a similar recommendation for the temporal pole? There doesn't seem to be any stats files apart from aparc concerning this region. Thanks! Mihaela

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Convert retenotopic areas from brainvoyger to Freesurfer
by Lilia Jorge 19 Apr '16

19 Apr '16

Hello I intend to compute cortical thickness in retinotopic areas. However retinotopic areas were delimited in BrainVoyager and the cortical thickness maps with FreeSurfer. There are any way to reconcile data from the two softawares? -- Com os melhores cumprimentos, Lília Jorge

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