Freesurfer July 2019

freesurfer@nmr.mgh.harvard.edu

104 participants
165 discussions

Re: [Freesurfer] Doubts in hippocampal subfields labeling
by Antonin Skoch 08 Jul '19

08 Jul '19

External Email - Use Caution Dear Eugenio, I have uploaded the subject as file hippocampal_subfields_labeling.tar.gz to your server surfer.nmr.mgh.harvard.edu. RAS coordinates of the unlabeled area are -31,-27,-9. Thank you in advance, Antonin Dear Antonin, It is difficult to see what’s going on in the images you sent. Would you mind uploading the subject, or at least sending us the image without the segmentation overlaid (and ideally, a sagittal view as well)? Cheers, /Eugenio-- Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com From: <freesurfer-boun...(a)nmr.mgh.harvard.edu> on behalf of Antonin Skoch <a...(a)ikem.cz> Reply-To: Antonin Skoch <a...(a)ikem.cz>, Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Date: Tuesday, 2 July 2019 at 21:43 To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] Doubts in hippocampal subfields labeling External Email - Use Caution Dear experts, I noticed that systematically in most of my subjects there is area in hippocampal region, labeled in aseg as hippocampus, but NOT labeled as hippocampus in hippocampal subfields segmentation (it has zero value there). See screenshots with norm.mgz overlaid by 1) aseg, 2) hippocampal subfields segmentation. According to T1 and T2 signal, it should neither be white matter and also probably not a ventricle/CSF. Neocortex is not located here. It has similar signal intensity as hippocampus, so I think that it should be hippocampus, but I am puzzled by hippocampal subfields segmentation results there. Why it is not labeled? Could you please help me to clarify this? My concern is to correctly label this area. I could upload the example subject if it is of any help. Regards, Antonin Skoch

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Re: [Freesurfer] Freesurfer Digest, Vol 185, Issue 11
by Mahshid Fouladivanda 08 Jul '19

08 Jul '19

External Email - Use Caution Dear Bruce, All the outputs are .nii and .gii I do not know if it is possible to convert it to the annotation! By the way, what is needed for creation of the annotation file? I mean what information, it needs? Regards Mahshid From: freesurfer-request(a)nmr.mgh.harvard.edu To: freesurfer(a)nmr.mgh.harvard.edu Date: Mon, 08 Jul 2019 11:34:24 -0400 Subject: Freesurfer Digest, Vol 185, Issue 11 Send Freesurfer mailing list submissions to freesurfer(a)nmr.mgh.harvard.edu To subscribe or unsubscribe via the World Wide Web, visit https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer or, via email, send a message with subject or body 'help' to freesurfer-request(a)nmr.mgh.harvard.edu You can reach the person managing the list at freesurfer-owner(a)nmr.mgh.harvard.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of Freesurfer digest..." Today's Topics: 1. Re: Skull Strip (Bruce Fischl) 2. How to Divide the Surface Parcellations of the Brain (Mahshid Fouladivanda) 3. Re: How to Divide the Surface Parcellations of the Brain (Bruce Fischl) 4. Assigning voxels different intensity values (Fotiadis, Panagiotis) 5. Re: Assigning voxels different intensity values (Bruce Fischl) 6. Re: Assigning voxels different intensity values (Fotiadis, Panagiotis) 7. Re: Assigning voxels different intensity values (Bruce Fischl) 8. Re: Assigning voxels different intensity values (Fotiadis, Panagiotis) 9. how to map regional t values on surface (fengmei fan) 10. Skull Strip (Admin) 11. Error in analyze (Qdec) (Abby tang) 12. Re: Freesurfer Digest, Vol 185, Issue 9 (vittal korann) 13. Postdoctoral Position opening at the University of Pittsburgh in neuroimaging of mood disorders (Anna Manelis) 14. Re: make_average_subject error: could not load norm volume from (null) (Greve, Douglas N.,Ph.D.) 15. Re: Skull Strip (Hoopes, Andrew) 16. Re: recon-all error: Correcting defect (Diamond, Bram Ryder) 17. Re: recon-all error: Correcting defect (Miguel ?ngel Rivas Fern?ndez) ---------------------------------------------------------------------- Message: 1 Date: Sun, 7 Jul 2019 13:33:35 -0400 (EDT) From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Skull Strip To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <alpine.LRH.2.20.1907071333050.916(a)door.nmr.mgh.harvard.edu> Content-Type: text/plain; charset="utf-8" I believe I already answered this. I don't understand what amplified noise you mean. The brainmask.mgz can be used with mri_mask to apply to any input volume you want. cheers Bruce On Sun, 7 Jul 2019, Admin wrote: > > ????????External Email - Use Caution???????? > > Dear Freesurfer group? Now,I want ?generated a brain mask including the brain but excluding the > amplified noise regions after skull strip, but I can't find the corresponding command line, so I > send this email to you,?hoping to get your help.? > My English is poor, if?I make mistakes ,?I hope you can understand me. Thanks for your help? > > > ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? > ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? Sincerely: Meng Nan Lin > ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? > ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? Date: 07/04/2019 > > > > > ? > > > > > ? > > > ------------------------------ Message: 2 Date: Mon, 08 Jul 2019 01:06:44 +0430 From: "Mahshid Fouladivanda" <M.Fouladivanda(a)sutech.ac.ir> Subject: [Freesurfer] How to Divide the Surface Parcellations of the Brain To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <WC20190707203644.661057(a)sutech.ac.ir> Content-Type: text/plain; charset="us-ascii" External Email - Use Caution Dear Freesurfer Experts, I would like to divide the surface parcellations of the neonatal brain. The parcells were extracted using Draw_EM (Developing brain Region Annotation With Expectation-Maximization), an atlas based segmentation, from cortical and sub-cortical. As I understand from help comments, mris_divide_parcellation would help, but it needs annotation file to be imported as input. I do not have the annotation file. I would appreciate it if you could help me how to divide my parcells in more regions? Regards, Mahshid

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recon-all error: Correcting defect
by Miguel Ángel Rivas Fernández 08 Jul '19

08 Jul '19

External Email - Use Caution I ran the recon-all in one subject and and this process was stopped in the topology correction. In particular during the "CORRECTING DEFECT 36 (vertices=19847, convex hull=5892, v0=94733)". I reviewed the lh.inflated.nofix and the lh.orig.nofix files in Freeview and I noticed that the this error would be located in the lh.inflated.nofix file. I am not completely sure but I suspect that this error may be due to the fact that there is a large amount of brain lesion and this would difficult the topology correction. How can I fix this problem? Thanks in advance. Best regards, -- *Miguel Ángel Rivas Fernández*

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Skull Strip
by Admin 08 Jul '19

08 Jul '19

External Email - Use Caution Dear Freesurfer group： just tried recon-all with the -use-gpu flag from the current development version of freesurfer (freesurfer-Linux-centos6_x86_64-dev-20161123-bb356e0), but it fail with the message that is cannot open libcudart.so.5.0. I have the current cuda version install(8.0). Does Freesurfer only work with cuda 5.0? Date: 07/08/2019

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Postdoctoral Position opening at the University of Pittsburgh in neuroimaging of mood disorders
by Anna Manelis 08 Jul '19

08 Jul '19

External Email - Use Caution Candidates are being considered for a post-doctoral associate position in the Anticipation, Cognition and Emotion lab ( www.ace.pitt.edu ) at the University of Pittsburgh (http://www.pitt.edu) to work with Dr. Anna Manelis and her team. A successful candidate will work on the NIMH funded research project that uses multimodal neuroimaging (fMRI, MRI, DTI and fNIRS) to understand the contribution of anticipatory processing to cognitive and emotional dysfunction in individuals with mood disorders. Pittsburgh is a vibrant community which promotes diversity and collaboration within its university and medical systems. Our lab works in conjunction with the University of Pittsburgh Medical Center to perform neuroimaging studies which will help us to better understand mood disorders, including major depressive disorder and bipolar disorders. *Required Qualification*s: we are seeking a highly motivated candidate with a PhD degree (or anticipated PhD degree) in psychology, cognitive neuroscience, computational neuroscience or a related discipline. A strong research background in the analysis and interpretation of neuroimaging data is required. A successful candidate will have excellent writing and communication skills. Candidates with a strong computational background are encouraged to apply. Experience with FSL, Freesurfer and E-prime is preferred. The ability to program in Shell, Matlab, Python and/or R is preferred. Experience with fNIRS, graph modeling and pattern classification analyses is a plus. While prior experience with clinical populations is not necessary, we expect candidates to be interested in neuroimaging research of working and episodic memory and/or anticipatory and emotional processing in individuals with mood disorders. *Responsibilities*: · Help to run fMRI/fNIRS experiments · Analyze fMRI, MRI, DTI and fNIRS neuroimaging data · Write manuscripts · Present findings from studies at conferences This is a full-time position that can be extended to 3 years. We are looking for someone to join our lab in Fall 2019 (with some flexibility). This position is funded by the NIMH and salary will vary based on experience. If you are interested in this position, please send a CV, research statement, preprints/reprints of papers, and the names and contact information for two references to *Anna Manelis (manelisa(a)upmc.edu <manelisa(a)upmc.edu>).*

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Re: [Freesurfer] Freesurfer Digest, Vol 185, Issue 9
by vittal korann 08 Jul '19

08 Jul '19

External Email - Use Caution Thanks, Tim for your reply. No, there is only "lh.pial" file exists not 'lh.pial_lgi. What might be the problem? Any help would be appreciated Thanks & regards -Korann On Sat, Jul 6, 2019 at 9:30 PM <freesurfer-request(a)nmr.mgh.harvard.edu> wrote: > Send Freesurfer mailing list submissions to > freesurfer(a)nmr.mgh.harvard.edu > > To subscribe or unsubscribe via the World Wide Web, visit > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > or, via email, send a message with subject or body 'help' to > freesurfer-request(a)nmr.mgh.harvard.edu > > You can reach the person managing the list at > freesurfer-owner(a)nmr.mgh.harvard.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Freesurfer digest..." > > > Today's Topics: > > 1. Re: [External] Re: rostral anterior cingulate fix? > (Zeng,Victor (BIDMC - Psychiatry)) > 2. Re: [External] Re: rostral anterior cingulate fix? (Bruce Fischl) > 3. Re: recon-all Error : inputs cannot have multiple frames. > ( Yueming ) > 4. Re: recon-all Error : inputs cannot have multiple frames. > (Bruce Fischl) > 5. error while running pial_lgi for gyrification index > (vittal korann) > 6. Re: error while running pial_lgi for gyrification index > (Tim Sch?fer) > 7. Viewing Uncorrected Significance Map in Freeview (Marie Hill) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 5 Jul 2019 17:42:28 +0000 > From: "Zeng,Victor (BIDMC - Psychiatry)" <vzeng(a)bidmc.harvard.edu> > Subject: Re: [Freesurfer] [External] Re: rostral anterior cingulate > fix? > To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: <1562348548910.95994(a)bidmc.harvard.edu> > Content-Type: text/plain; charset="iso-8859-1" > > > Sorry, I thought I attached something > Victor Zeng > Beth Israel Deaconess Medical Center > Keshavan Lab > ph: 617 754 1237 > -- > > ________________________________________ > From: freesurfer-bounces(a)nmr.mgh.harvard.edu < > freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Bruce Fischl < > fischl(a)nmr.mgh.harvard.edu> > Sent: Friday, July 5, 2019 10:24 AM > To: Freesurfer support list > Subject: [External] Re: [Freesurfer] rostral anterior cingulate fix? > > Hi Victor > > can you render the parcellation in that area on the surface (in freeview) > and show it to us? > > cheers > Bruce > > > On Fri, 5 Jul 2019, Zeng,Victor (BIDMC - Psychiatry) wrote: > > > > > Hi Freesurfer group - > > > > > > I'm using FS6.0 dev-20190118, and I'm processing a few brain scans. I'm > seeing a misparcellation of > > the right rostral anterior cingulate using tkmedit (I know tkmedit is > sorta deprecated), and it > > doesn't seem inappropriate to use control point fixes. How would you > best fix this (I'm open to > > using freeview), without just editing the aparc+aseg.mgz? > > > > > > Victor Zeng > > Beth Israel Deaconess Medical Center > > Keshavan Lab > > ph: 617 754 1237 > > -- > > > > > ____________________________________________________________________________________________________ > > > > This message is intended for the use of the person(s) to whom it may be > addressed. It may contain > > information that is privileged, confidential, or otherwise protected > from disclosure under > > applicable law. If you are not the intended recipient, any > dissemination, distribution, copying, or > > use of this information is prohibited. If you have received this message > in error, please > > permanently delete it and immediately notify the sender. Thank you. > > > > >

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Error in analyze (Qdec)
by Abby tang 08 Jul '19

08 Jul '19

External Email - Use Caution Hello FreeSurfer Developers, I want to compare the relationship between age and thickness, which is controlled the effect about sex,education and eTIV, so QDEC was used. However I met a problem when I use it, such as picture1. I get the wrong message, Error in Analyze: command failed: mri_glmfit --y /home/abby/Desktop/qdecyoung/qdec/Untitled/y.mgh --fsgd /home/abby/Desktop/qdecyoung/qdec/Untitled/qdec.fsgd dods --glmdir /home/abby/Desktop/qdecyoung/qdec/Untitled --surf fsaverage lh --label /home/abby/Desktop/qdecyoung/fsaverage/label/lh.aparc.label --C /home/abby/Desktop/qdecyoung/qdec/Untitled/contrasts/lh-Avg-Intercept-thickness.mat --C /home/abby/Desktop/qdecyoung/qdec/Untitled/contrasts/lh-Avg-thickness-age-Cor.mat --C /home/abby/Desktop/qdecyoung/qdec/Untitled/contrasts/lh-Diff-Female-Male-Intercept-thickness.mat --C /home/abby/Desktop/qdecyoung/qdec/Untitled/contrasts/lh-Diff-Female-Male-Cor-thickness-age.mat. So I tried to put those to terminal, the feedback is: gdfRead(): reading /home/abby/Desktop/qdecyoung/qdec/Untitled/qdec.fsgd INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done. Continuous Variable Means (all subjects) 0 age 80.3537 2.43637 1 education 12.189 3.6099 2 eTIV 1.33934e+06 242446 Class Means of each Continuous Variable 1 sexFemale 80.0568 11.4773 1265564.4638 2 sexMale 80.6974 13.0132 1424768.7681 INFO: gd2mtx_method is dods Reading source surface /usr/local/freesurfer/subjects/fsaverage/surf/lh.white Number of vertices 163842 Number of faces 327680 Total area 65416.984375 AvgVtxArea 0.399269 AvgVtxDist 0.721953 StdVtxDist 0.195470 $Id: mri_glmfit.c,v 1.241.2.4 2016/12/08 22:02:40 zkaufman Exp $ cwd /home/abby/Desktop/qdecyoung/qdec cmdline mri_glmfit.bin --y /home/abby/Desktop/qdecyoung/qdec/Untitled/y.mgh --fsgd /home/abby/Desktop/qdecyoung/qdec/Untitled/qdec.fsgd dods --glmdir /home/abby/Desktop/qdecyoung/qdec/Untitled --surf fsaverage lh --label /home/abby/Desktop/qdecyoung/fsaverage/label/lh.aparc.label --C /home/abby/Desktop/qdecyoung/qdec/Untitled/contrasts/lh-Avg-Intercept-thickness.mat --C /home/abby/Desktop/qdecyoung/qdec/Untitled/contrasts/lh-Avg-thickness-age-Cor.mat --C /home/abby/Desktop/qdecyoung/qdec/Untitled/contrasts/lh-Diff-Female-Male-Intercept-thickness.mat --C /home/abby/Desktop/qdecyoung/qdec/Untitled/contrasts/lh-Diff-Female-Male-Cor-thickness-age.mat sysname Linux hostname abby-virtual-machine machine x86_64 user abby FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 0 y /home/abby/Desktop/qdecyoung/qdec/Untitled/y.mgh logyflag 0 usedti 0 FSGD /home/abby/Desktop/qdecyoung/qdec/Untitled/qdec.fsgd labelmask /home/abby/Desktop/qdecyoung/fsaverage/label/lh.aparc.label maskinv 0 glmdir /home/abby/Desktop/qdecyoung/qdec/Untitled IllCondOK 0 ReScaleX 1 DoFFx 0 Creating output directory /home/abby/Desktop/qdecyoung/qdec/Untitled Loading y from /home/abby/Desktop/qdecyoung/qdec/Untitled/y.mgh ... done reading. INFO: gd2mtx_method is dods Saving design matrix to /home/abby/Desktop/qdecyoung/qdec/Untitled/Xg.dat Computing normalized matrix Normalized matrix condition is 9294.65 Matrix condition is 1e+08 Found 148151 points in label. Pruning voxels by thr: 1.175494e-38 Found 139197 voxels in mask Saving mask to /home/abby/Desktop/qdecyoung/qdec/Untitled/mask.mgh Reshaping mriglm->mask... search space = 69257.619818 DOF = 156 Starting fit and test Fit completed in 0.338183 minutes Computing spatial AR1 on surface Residual: ar1mn=0.995542, ar1std=0.000996, gstd=6.054132, fwhm=14.256391 Writing results lh-Avg-Intercept-thickness maxvox sig=10.0394 F=48.3686 at index 13210 0 0 seed=1563457975 MatrixMultiplyD(): m2 is null break matrix.c:415 No such file or directory When same operations were did with other files, Qdec running normally. I don't know why. Please help me. Thank you Best regards abby

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how to map regional t values on surface
by fengmei fan 08 Jul '19

08 Jul '19

External Email - Use Caution Dear all, I have used the command to calculate mean thickness: aparcstats2table ―subjectsfile ${subjects_list} ―parc aparc.a2009s ―hemi lh ―meas ${meas} ―tablefile aparc.a2009s.${meas}.lh.txt aparcstats2table ―subjectsfile ${subjects_list} ―parc aparc.a2009s ―hemi rh ―meas ${meas} ―tablefile aparc.a2009s.${meas}.rh.txt And when i have t/r values for each region (74 per hemisphere), how to map them on surface? like this one with colorbar representing t/r values? [cid:_Foxmail.1@e5e8b321-1060-adcd-7310-68f457c85a95] Best, Fengmei ________________________________ fanfengmei(a)live.com

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Assigning voxels different intensity values
by Fotiadis, Panagiotis 07 Jul '19

07 Jul '19

Hello, I was wondering whether there is a way to assign a different intensity value on each voxel within a parcellation file (such as aseg.mgz). What I’m essentially trying to do is create a file (using the aseg.mgz file as a template) where each voxel represents a different ROI. I can think of a way to do that in Freeview for each individual voxel but I wasn’t sure whether there was a more efficient/automated way in either bash or matlab. Let me know if the above doesn’t make any sense, and thanks in advance! Best, Panos

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How to Divide the Surface Parcellations of the Brain
by Mahshid Fouladivanda 07 Jul '19

07 Jul '19

External Email - Use Caution Dear Freesurfer Experts, I would like to divide the surface parcellations of the neonatal brain. The parcells were extracted using Draw_EM (Developing brain Region Annotation With Expectation-Maximization), an atlas based segmentation, from cortical and sub-cortical. As I understand from help comments, mris_divide_parcellation would help, but it needs annotation file to be imported as input. I do not have the annotation file. I would appreciate it if you could help me how to divide my parcells in more regions? Regards, Mahshid

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Freesurfer July 2019