Freesurfer

freesurfer@nmr.mgh.harvard.edu

30132 discussions

Freeview Surface Loading View Center
by Mingjian He 21 Jan '20

21 Jan '20

Hi, When using Freeview to load a surface file without volume, how does Freeview set the initial view center and cursor position? I’ve checked mid point of xyz ranges, centroid of vertices, and median. None of these gives me the initial SurfaceRAS values when opening the surface with Freeview. Thank you! Best, Alex External Email - Use Caution

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recon exited with errors
by Desel, Tenzin 21 Jan '20

21 Jan '20

Hello FreeSurfer Developers, I'm attempting to run recon-all after unpacking data. It is exiting with errors - mri_cc: no WM voxels found with norm > 40 -- check skull stripping I've attached the recon-all.log in case it's of any use. 1) FreeSurfer version: freesurfer-Linux-centos7_x86_64-stable-v6-20161229-80ac5eb 2) Platform: centos7_x86_64 3) uname -a: Linux lemmiwinks.nmr.mgh.harvard.edu 3.10.0-1062.4.3.el7.x86_64 #1 SMP Wed Nov 13 23:58:53 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux 4) recon-all.log: see attached Thank you!

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Input PET images for PetSurfer Analysis
by Ferraro, Pilar 21 Jan '20

21 Jan '20

External Email - Use Caution Dear Freesurfer experts, I am starting a new analysis using PetSurfer to evaluate the effect of different PVC corrections on brain metabolism in a set of patients. I have already analyzed all the T1 MRI data using the normal stream, however I have never worked on PET data before. I have the original DICOMS from a static PET acquisition but I’d like to know more about the preprocessing steps needed for these PET data. I am thinking I should simply convert PET DICOMS to NifTI, normalize them to a standard template and then smooth them with 8- mm full width at half maximum Gaussian Kernel to obtain the input images for the PetSurfer analysis. Am I correct or should I add further preprocessing steps? Thanks, Pilar Il giorno 16 gen 2020, alle ore 6:00 PM, freesurfer-request(a)nmr.mgh.harvard.edu<mailto:freesurfer-request@nmr.mgh.harvard.edu> ha scritto: Send Freesurfer mailing list submissions to freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@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. Qdec and TkSurfer input boxes (Marcos Martins da Silva) 2. FreeSurfer analyses in MatLab (Graduate Imaging) 3. Re: Oval shape in average subject inflated (Marina Fern?ndez) 4. Segfault in mris_topo_fixer (Christian O'Reilly, Dr) 5. Re: Segfault in mris_topo_fixer (Hoopes, Andrew) 6. Segmentation Fault during recon-all using FLAIR Image (Swanson,Clayton) ---------------------------------------------------------------------- Message: 1 Date: Wed, 15 Jan 2020 14:02:26 -0300 From: Marcos Martins da Silva <marcosm(a)hucff.ufrj.br> Subject: [Freesurfer] Qdec and TkSurfer input boxes To: freesurfer <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <CANXLKP7HxjOjLShobVkYr+eDGNuh+PksDM1Aio=9XgKm_NaXeg(a)mail.gmail.com> Content-Type: text/plain; charset="utf-8" External Email - Use Caution Hi! I use FreeSurfer 6.0 over CentOS 7. I have just notice a problem with input/entry/edit boxes in Qdec and TkSurfer. I can see box content, click inside the box and even select the content but it seems read only: I can't change it. So it is impossible to see the scatter plot from a specific vertex inputing its number. Any clue about what happened and how to fix it? Thank you for your attention. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20200115/1… ------------------------------ Message: 2 Date: Wed, 15 Jan 2020 16:08:12 -0500 From: Graduate Imaging <graduate.imaging(a)gmail.com> Subject: [Freesurfer] FreeSurfer analyses in MatLab To: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <CA+yW3sSV=E5M1_cbOJfecPMCeCePjtZy_isFL8vzmRMDX55Pfw(a)mail.gmail.com> Content-Type: text/plain; charset="utf-8" External Email - Use Caution Hello, I recently ran a vertex wise analysis on two different projects the first had three groups with three co-variates that looked at if group membership was associated with brain volume. The second project had two groups with three co-variates looking at psychiatric x BMI interaction effect on brain volume. I'm interested in running ROI analyses in matlab to ensure the same matrices were used. To run the ROI analyses I'm going to important the design matrix from the vertex wise analysis and use the fast_glmfit and fast_fratio commands as shown below: X = load('Xg.dat'); C = load('C.dat'); y = load('ROI.dat'); text file containing participant ROI values from the DKT atlas. [beta rvar] = fast_glmfit(y,X); [F pvalues] = fast_fratio(beta,X,rvar,C My first question is the beta values that are calculated from fast_glmfit are unstandardized is there anyway way to have it compute standardized values? My second question is when I ran the ROI analyses looking at the diagnosis x BMI interaction effect it outputs an array of beta values for each regressor. In addition to each groups beta value (for BMI) I'm interested in the beta value of the interaction (ie diagnosis x BMI). I was wondering how do i go about obtaining this? Would I have to create a new matrix with the interaction term included in it? If so would the analysis essentially be one group with the diagnosis x BMI interaction term plus the three co-variates? -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20200115/1… ------------------------------ Message: 3 Date: Thu, 16 Jan 2020 12:58:41 +0100 From: Marina Fern?ndez <marina.fdez.alvarez(a)gmail.com> Subject: Re: [Freesurfer] Oval shape in average subject inflated To: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <CAALjZmeP2eKby4GGLJn_X6uOfCwPgNfnE3WUq5kmbv0-nqHi6Q(a)mail.gmail.com> Content-Type: text/plain; charset="utf-8" External Email - Use Caution It works! Thank you very much Bruce! -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20200116/1… ------------------------------ Message: 4 Date: Thu, 16 Jan 2020 14:57:00 +0000 From: "Christian O'Reilly, Dr" <christian.oreilly(a)mcgill.ca> Subject: [Freesurfer] Segfault in mris_topo_fixer To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <YQBPR0101MB10125047A377D0AD8F34D349E1360(a)YQBPR0101MB1012.CANPRD01.PROD.OUTLOOK.COM> Content-Type: text/plain; charset="iso-8859-1" External Email - Use Caution Hi, I got the following error running mris_topo_fixer: ~$ mris_topo_fixer -mgz -warnings ANTS6-0Months3T lh INFO: assuming .mgz format verbose mode on (medium mode): printing warnings reading input surface /usr/local/freesurfer/subjects/ANTS6-0Months3T/work/ANTS6-0Months3T/surf/lh.orig... Before topology correction, eno=0 (nv=43656, nf=87312, ne=130968, g=1) Surface Diagnostics: eno=0 (nv=43656, nf=87312, ne=130968) # of border vertices [ #v ~ #f ] 0 # of edges with single face 0 # of edges with more than 2 faces 0 # of corner configurations 0 The original surface is a valid manifold Counting the number of connected components The original surface has one component The original surface does not self-intersect The surface has 1 loops (X=0) Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 10 iterations identify defects... marking ambiguous vertices... 1527 ambiguous faces found in tessellation segmenting defects... analyzing defects for overlaps... reading brain volume from brain... reading wm segmentation from wm... Detecting contrast direction: right direction [ GM (129.46) < WM (134.73) ] ASSERTION FAILED: /local_mount/space/terrier/2/terrier_nightly_build/trunk/ah221-infant/utils/mrisurf_topology.c:1002 vt->nsizeMax > 0 ASSERTION FAILED: /local_mount/space/terrier/2/terrier_nightly_build/trunk/ah221-infant/utils/mrisurf_topology.c:1002 vt->nsizeMax > 0 Segmentation fault (core dumped) Any idea what in the data file could cause the assert "vt->nsizeMax > 0" to be triggered? Any idea how to go around it? Thank you, Christian -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20200116/8… ------------------------------ Message: 5 Date: Thu, 16 Jan 2020 15:39:32 +0000 From: "Hoopes, Andrew" <AHOOPES(a)mgh.harvard.edu> Subject: Re: [Freesurfer] Segfault in mris_topo_fixer To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <BN8PR04MB56979DB2BBFD5A0BAB3E280EF9360(a)BN8PR04MB5697.namprd04.prod.outlook.com> Content-Type: text/plain; charset="us-ascii" Hi Christian, if you send me that surface, I can take a look at what's going wrong. best Andrew ________________________________________ From: freesurfer-bounces(a)nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Christian O'Reilly, Dr <christian.oreilly(a)mcgill.ca> Sent: Thursday, January 16, 2020 9:57 AM To: freesurfer(a)nmr.mgh.harvard.edu Subject: [Freesurfer] Segfault in mris_topo_fixer External Email - Use Caution Hi, I got the following error running mris_topo_fixer: ~$ mris_topo_fixer -mgz -warnings ANTS6-0Months3T lh INFO: assuming .mgz format verbose mode on (medium mode): printing warnings reading input surface /usr/local/freesurfer/subjects/ANTS6-0Months3T/work/ANTS6-0Months3T/surf/lh.orig... Before topology correction, eno=0 (nv=43656, nf=87312, ne=130968, g=1) Surface Diagnostics: eno=0 (nv=43656, nf=87312, ne=130968) # of border vertices [ #v ~ #f ] 0 # of edges with single face 0 # of edges with more than 2 faces 0 # of corner configurations 0 The original surface is a valid manifold Counting the number of connected components The original surface has one component The original surface does not self-intersect The surface has 1 loops (X=0) Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 10 iterations identify defects... marking ambiguous vertices... 1527 ambiguous faces found in tessellation segmenting defects... analyzing defects for overlaps... reading brain volume from brain... reading wm segmentation from wm... Detecting contrast direction: right direction [ GM (129.46) < WM (134.73) ] ASSERTION FAILED: /local_mount/space/terrier/2/terrier_nightly_build/trunk/ah221-infant/utils/mrisurf_topology.c:1002 vt->nsizeMax > 0 ASSERTION FAILED: /local_mount/space/terrier/2/terrier_nightly_build/trunk/ah221-infant/utils/mrisurf_topology.c:1002 vt->nsizeMax > 0 Segmentation fault (core dumped) Any idea what in the data file could cause the assert "vt->nsizeMax > 0" to be triggered? Any idea how to go around it? Thank you, Christian ------------------------------ Message: 6 Date: Thu, 16 Jan 2020 15:55:44 +0000 From: "Swanson,Clayton" <Clayton.Swanson(a)colostate.edu> Subject: [Freesurfer] Segmentation Fault during recon-all using FLAIR Image To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <A95D6E27-F818-45F7-9391-C5B130978013(a)colostate.edu> Content-Type: text/plain; charset="us-ascii" External Email - Use Caution Hello FreeSurfer Developers, I am attempting to perform a recon-all using a T2-FLAIR image. I have already run this particular participant through recon-all with their T1 image without error. While running the recon-all using the T2 the process exited with error stating a segmentation fault. Is there any way to run fix this problem on my end or better understand why this would be occurring? I have uploaded the recon-all.log for your convenience. Thank you, Clayton ________________________________ Clayton Swanson MS Graduate Research Assistant & PhD Student Sensorimotor Neuroimaging Laboratory Colorado State University Office: (970) 491-6160 Clayton.Swanson(a)colostate.edu<mailto:Clayton.Swanson@colostate.edu> -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20200116/2… -------------- next part -------------- A non-text attachment was scrubbed... Name: recon-all.log Type: application/octet-stream Size: 188509 bytes Desc: recon-all.log Url : http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20200116/2… ------------------------------ _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer End of Freesurfer Digest, Vol 191, Issue 22 *******************************************

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Change the subject ID after recon-all?
by Tim Schäfer 21 Jan '20

21 Jan '20

External Email - Use Caution Dear FreeSurfer experts, I have two questions on subject IDs in FreeSurfer output. 1) is it possible to change to subject identifier in the FreeSurfer output after recon-all has been run? Background: I would like to upload data pre-processed with FreeSurfer to a consortium server. The subject ID is a random identifier, but the upload guidelines say this identifier must only occur in certain file types (Excel files, .log files, and some more, but not in any other files). I noticed that a lot of the output files produced by FreeSurfer contain the subject identifier somewhere, including various binary files, so I guess there is no easy way to change it. But maybe there is? Like rerunning a part of recon-all? 2) If not, I could rename the source NIFTI files (e.g., from the identifiers to something like 'subject001', 'subject002', ...) and re-process everything. This would take some computational time for the > 500 subjects, but it would be okay I guess. But a large number of the subjects have manual edits applied already. Is there a way to keep the manual edits? E.g., I thought maybe I could rename the individual directories of the edited subjects, leave the edited files in there, and run recon-all again. But what would happen? Will the new output files have the renamed ID from the directory name (and thus the recon-all command line), or will they still use the old ID (from the header of the existing files)? Or will the existing, edited files which contain a different ID be ignored during the new run because the IDs do not match, and thus the existing edits would have no effect? All the best, Tim -- Dr. Tim Schäfer Postdoc Computational Neuroimaging Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany

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question about curv.mgh
by Raffaele Dubbioso 21 Jan '20

21 Jan '20

External Email - Use Caution Hello FS team, can you please tell me what is the measurement scale of the curv.mg file? Is it a mean curvature (mm-1) or a gaussian curvature (mm-2)? I got values between 0.02 and -0.08 and it seems they are gaussian curvature. Thanks a lot for your help Best regards Rafael

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Re: [Freesurfer] freesurfer fornix
by Annink, K.V. 20 Jan '20

20 Jan '20

External Email - Use Caution Dear all, I have a question about the fornix segmentation. First I have used the comment mri_cc -f to create fornix.mgz. After all files were created, I have used mri_segstats to create the stats file. Is this correct? In the output file the nvoxes and volume are the same. Thank you for your help. Kind regards, Kim # VoxelVolume_mm3 1 # TableCol 1 ColHeader Index # TableCol 1 FieldName Index # TableCol 1 Units NA # TableCol 2 ColHeader SegId # TableCol 2 FieldName Segmentation Id # TableCol 2 Units NA # TableCol 3 ColHeader NVoxels # TableCol 3 FieldName Number of Voxels # TableCol 3 Units unitless # TableCol 4 ColHeader Volume_mm3 # TableCol 4 FieldName Volume # TableCol 4 Units mm^3 # TableCol 5 ColHeader StructName # TableCol 5 FieldName Structure Name # TableCol 5 Units NA # NRows 1 # NTableCols 5 # ColHeaders Index SegId NVoxels Volume_mm3 StructName 1 250 465 465.0 Fornix ------------------------------------------------------------------------------ De informatie opgenomen in dit bericht kan vertrouwelijk zijn en is uitsluitend bestemd voor de geadresseerde. Indien u dit bericht onterecht ontvangt, wordt u verzocht de inhoud niet te gebruiken en de afzender direct te informeren door het bericht te retourneren. Het Universitair Medisch Centrum Utrecht is een publiekrechtelijke rechtspersoon in de zin van de W.H.W. (Wet Hoger Onderwijs en Wetenschappelijk Onderzoek) en staat geregistreerd bij de Kamer van Koophandel voor Midden-Nederland onder nr. 30244197. Denk s.v.p aan het milieu voor u deze e-mail afdrukt. ------------------------------------------------------------------------------ This message may contain confidential information and is intended exclusively for the addressee. If you receive this message unintentionally, please do not use the contents but notify the sender immediately by return e-mail. University Medical Center Utrecht is a legal person by public law and is registered at the Chamber of Commerce for Midden-Nederland under no. 30244197. Please consider the environment before printing this e-mail.

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20 Jan '20

Hi everyone, This is a reminder that registration for the Spring 2020 FreeSurfer course will open TOMORROW (Tuesday, January 21st) at 10:30am EST! At that time, the link to the registration page will appear on the course website: https://surfer.nmr.mgh.harvard.edu/fswiki/CourseDescription The four-day course will run from March 30th through April 2nd, 2020 at the Massachusetts General Hospital Martinos Center for Biomedical Imaging in Charlestown, Massachusetts. The schedule for this course has not been finalized but an example schedule can be found on the course website: https://surfer.nmr.mgh.harvard.edu/fswiki/CourseDescription How to get a spot in the course -Easy! Register on the day we open registration & submit an accepted form of payment by the deadline. Some reasons why people are unable to attend the course: -Waiting too long to register. The 50 seats in the course usually fill up within a day or two. -Waiting too long before requesting a check from their institution. (Make sure you put in the request for a check immediately *after* you register.) -Not realizing cash payments must also be made by the deadline. (MoneyGram or Western Union transfers are accepted as well as personal deliveries.) -Booking flights, sending in payment, and/or just showing up without registering for the course or moving up from the waiting list! For questions about the course, you'll likely find answers on the course website. If you don't find what you're looking for, feel free to email the course organizers at freesurferlab(a)gmail.com. If you would like to hear about future course dates, sign up for the course mailing list here<http://surfer.nmr.mgh.harvard.edu/cgi-bin/fsurfer/interest.cgi>. ------------------ FreeSurfer Course Organizers Massachusetts General Hospital Athinoula A. Martinos Center for Biomedical Imaging Bldg. 149, 13th Street Charlestown, MA 02129 Phone: (617) 726-6598

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Re: [Freesurfer] Unable to run recon all
by Greve, Douglas N.,Ph.D. 20 Jan '20

20 Jan '20

It is not clear why it failed for these subjects (always happens at the same place). Can you upload one of them for me to take a look at? here are the instructions From the linux command line, Create the file you want to upload, eg, cd $SUBJECTS_DIR tar cvfz subject.tar.gz ./subject Now log into our anonymous FTP site: ftp surfer.nmr.mgh.harvard.edu It will ask you for a user name: use "anonymous" (no quotes) It will ask you for a password: use "anonymous" (no quotes) cd transfer/incoming binary put subject.tar.gz Send an email that the file has been and the name of the file. On 1/6/20 11:49 AM, Sahil Bajaj wrote: > > External Email - Use Caution > > Hi Dough, > > I finished recon -all on about 515 subjects and I get error in 11 out > of 515 subjects. Here I am attaching recon-all.log files of all those > 11 subjects. I would really appreciate your help in fixing these errors. > > Thanks, > Sahil > > On Thu, Jan 2, 2020 at 10:03 AM Greve, Douglas N.,Ph.D. > <DGREVE(a)mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> wrote: > > Can you send the recon-all.log file? You sent the .error file > > On 12/20/2019 10:13 AM, Sahil Bajaj wrote: >> >> External Email - Use Caution >> >> Hello FS experts, >> >> I am trying to run recon all on about 100 subjects. But one out >> of 100 subjects finishes recon all with error, and doesn't >> complete the process. Here I am attaching recon all log for your >> reference. Also, before installing freesurfer on MAC Catalina, I >> ran sudo spctl - -master -disable >> >> I would really appreciate any help in resolving this. >> >> Thanks, >> Sahil >> 1) FreeSurfer version: >> >> freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c >> >> 2) Platform: MACOS Catalina >> 3) recon-all.log: see attached >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >> 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 >

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Re: [Freesurfer] Freesurfer Digest, Vol 191, Issue 29
by Devika K 19 Jan '20

19 Jan '20

External Email - Use Caution I tried by specicying the subjects name, by following the below command. aparcstats2table --hemi lh \ --subjects 004 021 040 067 080 092 \ --meas thickness \ --parc aparc.a2009s \ --tablefile lh.aparc.a2009.thickness.tabl But still I got the same error. On Sun, Jan 19, 2020, 10:30 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. RES: Re: freesurfer container - freeview error > (marcosm(a)hucff.ufrj.br) > 2. registration of dwi images (Sam W) > 3. Re: registration of dwi images (Yendiki, Anastasia) > 4. Project hippocampus to inflated 3D model? (Mohammad Rashid) > 5. Re: aparcstats2table error (Devika K) > 6. Re: Project hippocampus to inflated 3D model? (Bruce Fischl) > 7. Re: aparcstats2table error (Bruce Fischl) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Sat, 18 Jan 2020 15:05:15 -0300 > From: <marcosm(a)hucff.ufrj.br> > Subject: [Freesurfer] RES: Re: freesurfer container - freeview error > To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: <5e2383f1.1c69fb81.cfdf5.57cf(a)mx.google.com> > Content-Type: text/plain; charset="us-ascii" > > An HTML attachment was scrubbed... > URL: > http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20200118/f… > > ------------------------------ > > Message: 2 > Date: Sun, 19 Jan 2020 00:52:10 +0100 > From: Sam W <samfmri(a)gmail.com> > Subject: [Freesurfer] registration of dwi images > To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: > < > CAFYEHVvrxw-P0VWvqeiA_fMnUrMavmSb9wts3zDhLGFVZHC2ow(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > External Email - Use Caution > > Hello! > I have run eddy on all my dwi images and then run bbregister using the > first b0 image as the source image. > The b0 image is now well aligned with the anatomical image but how can I > apply the same transformation to all other dwi images in my dataset? > > After eddy correction I extracted the first b0 image (nodif.nii.gz) and run > the bbregister command: > bbregister --s sub001 --mov /home/samm/nodif.nii.gz --reg > /home/samm/nodiffb2orig.dat --dti --init-fsl --o > /home/samm/registered_b0.nii.gz > > Thanks! > Sam >

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Project hippocampus to inflated 3D model?
by Mohammad Rashid 19 Jan '20

19 Jan '20

External Email - Use Caution Hello, I have had success projecting regions such as the entorhinal region to an inflated 3D model. But I can't seem to do the same for hippocampi. I wouldn't need any hippocampal subfields, just projecting the hippocampus as a whole would be useful. Is there perhaps a particular file used for this that I am missing? Any help is appreciated, Mohammad Rashid

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