Freesurfer

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Re: [Freesurfer] Ghosting Artifact
by Harms, Michael 27 Jan '17

27 Jan '17

That subjects looks like a candidate for exclusion, because the SNR anteriorly is much less than posteriorly. It looks to me like there is either a problem with your head coil, or the anterior coil elements were not active. cheers, -MH -- Michael Harms, Ph.D. ----------------------------------------------------------- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave. Tel: 314-747-6173 St. Louis, MO 63110 Email: mharms(a)wustl.edu From: <freesurfer-bounces(a)nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu>> on behalf of "Fotiadis, Panagiotis" <PFOTIADIS(a)mgh.harvard.edu<mailto:PFOTIADIS@mgh.harvard.edu>> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Date: Friday, January 27, 2017 at 12:30 PM To: "freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>" <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Subject: [Freesurfer] Ghosting Artifact Hello, I have a T1 weighted scan with a semi-severe ghosting artifact, and recon-all is not able to complete the reconstruction process (according to recon-all log, it tries to fix 237 defects and at defect 209 the recon stops). Is there anything that I can do to recover the scan so I can reconstruct it successfully? (I have attached a few pics indicating the artifact). Thanks in advance for your time! Best, Panos Panagiotis Fotiadis Research Technologist II J. P. Kistler Stroke Research Center Massachusetts General Hospital 175 Cambridge Street, Suite 300 Boston, MA, 02114 T: (617) 643-3869 ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

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Ghosting Artifact
by Fotiadis, Panagiotis 27 Jan '17

27 Jan '17

Hello, I have a T1 weighted scan with a semi-severe ghosting artifact, and recon-all is not able to complete the reconstruction process (according to recon-all log, it tries to fix 237 defects and at defect 209 the recon stops). Is there anything that I can do to recover the scan so I can reconstruct it successfully? (I have attached a few pics indicating the artifact). Thanks in advance for your time! Best, Panos Panagiotis Fotiadis Research Technologist II J. P. Kistler Stroke Research Center Massachusetts General Hospital 175 Cambridge Street, Suite 300 Boston, MA, 02114 T: (617) 643-3869

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White matter probability map.
by miracooloz＠gmail.com 27 Jan '17

27 Jan '17

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Cortical volume from masked region
by Eli Johnson 27 Jan '17

27 Jan '17

Hi all, I am trying to extract the volume from a FreeSurfer segmented scan within a pre-registered mask region, but only within the cortex, and wanted to check my command. The mask is a binary mask (value of 1 across the mask) and is in the same space as the orig.mgz file. It covers part of the frontal lobe. I have run: mri_segstats --seg ./scan500_std/mri/500_lobes_1-in-fs.mgz --id 1 --i ./scan500_std/mri/aparc+aseg.mgz --accumulate --sum test.reg1.sum This has output a text file with a value of 495563 mm3 in the last row. I wanted to check whether this is the correct command to extract only cortical GM within this mask. If this is correct, should be adding other flags (e.g. -pv). I have searched the mailing list and the options for mri_segstats, but I'm not 100% confident in what I've done - so any tips would be greatly appreciated. Many thanks Eli

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PETsurf - point-spread function in ADNI
by Eduard Vilaplana Martinez 27 Jan '17

27 Jan '17

Dear Freesurfer experts, I'm processing ADNI PET data (AV45 and AV1451) in a surface-based approach following your guidelines (https://surfer.nmr.mgh.harvard.edu/fswiki/PetSurfer) Do you guys have any experience with ADNI data? I would like to apply partial volume correction but I don't know which is the FWHM of the point-spread function. I'm taking the most pre-processed images (i.e. co-reg, avg, std image and vox siz, uniform resolution), and ADNI say that "Each image set is filtered with a scanner-specific filter function (can be a non-isotropic filter) to produce images of a uniform isotropic resolution of 8 mm FWHM, the approximate resolution of the lowest resolution scanners used in ADNI." Would using a 8mm FWHM for the PV correction be a correct approach? Any help would be greatly appreciated. Thanks in advance Edu V.

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find surface coordinates in MNI space
by Jacobs H (NP) 27 Jan '17

27 Jan '17

Dear FreeSurfers, I am trying to locate certain regions from the Desikan atlas on a MNI surface (Brainnet-viewer) . How can I convert coordinates in surface space to MNI coordinates and are these the regular coordinates (RAS)? Many thanks. Heidi

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label to vol
by francesca bottino 27 Jan '17

27 Jan '17

Dear FS's experts, I have this problem: I want transform a volume file .nii in surfaces files .label. I had tried the command cor2label but I don't know very well how to use it. Please help me. Tnks ________________________________ Da: freesurfer-bounces(a)nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> per conto di freesurfer-request(a)nmr.mgh.harvard.edu <freesurfer-request(a)nmr.mgh.harvard.edu> Inviato: giovedì 26 gennaio 2017 18.00 A: freesurfer(a)nmr.mgh.harvard.edu Oggetto: Freesurfer Digest, Vol 155, Issue 41 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 Freesurfer Info Page - mail.nmr.mgh.harvard.edu<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> mail.nmr.mgh.harvard.edu To see the collection of prior postings to the list, visit the Freesurfer Archives. A searchable archive which of messages PRIOR to March 2004 is at ... 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. Longitudinal stream with v6 but cross with v5.3 (Matthieu Vanhoutte) 2. Re: Hippocampal Subfields Segmentation Error (Iglesias Gonzalez, Eugenio) 3. Re: longitudinal tracula error (Yendiki, Anastasia) 4. Re: freesurfer 6.0 with some of the analyses (Rizvi, Batool) 5. Re: Command for Reverse Normalizing with mri_vol2vol Using CVS m3z Morphs (Lilla Zollei) 6. Re: freesurfer 6.0 with some of the analyses (Adam Martersteck) 7. Re: freesurfer 6.0 with some of the analyses (Iglesias Gonzalez, Eugenio) ---------------------------------------------------------------------- Message: 1 Date: Thu, 26 Jan 2017 09:58:30 +0100 From: Matthieu Vanhoutte <matthieuvanhoutte(a)gmail.com> Subject: [Freesurfer] Longitudinal stream with v6 but cross with v5.3 To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <CAF6uKJSd96orkeH+WWX5T6jz3xeYtTNiJ80i96C_5do1L8CWqA(a)mail.gmail.com> Content-Type: text/plain; charset="utf-8" Dear FS's experts, I have run all my cross with v5.3 and hesitate to run all longitudinal process with v6. Does that make sense and will improve the process or would it be risky to do this ? Many thanks for your lights ! Best regards, Matthieu

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Confusion while planning analysis on QDEC
by Vikas Bandalli 27 Jan '17

27 Jan '17

Dear Freesurfer developers, I had a small confusion while performing a paired analysis. An analysis is to be performed to examine or analyze the structural differences between two group 'Control' and 'Patient' subjects. If my study is age and sex matched, say there is a control with same age and sex for every patient, How should I plan my analysis on QDEC, I am currently following this pattern, *Fixed fatcor :- Diagnosis (normal or patient)Continous factor* :- *Age * *Nuisance factor *:- *Total ICV* Is this a correct design? or should I add *sex * to the *fixed factor,* i.e, *fixed factor :- Diagnosis & Sex * How will my analysis vary with and without using sex as fixed factor ? Which is the correct design? Thank you very much in advance. Regards, Vikas Bandalli Raju -- Vikas B. R. Medical student Bangalore Medical College and Research Institute (BMCRI), Bangalore,India, Ph : +918904286825

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Registration: Variable Must Begin with a Letter Error
by Anderson Napolitano 27 Jan '17

27 Jan '17

?Thank you Dr. Greve and Don. Unfortunately adding '\' after spaces and removing the spaces all together doesn't seem to resolve the said error.

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Hippocampal Subfields Segmentation Error
by Michel Hu 27 Jan '17

27 Jan '17

Dear Freesurfer Developers, For my research I'm trying to run the hippocampal subfield segmentation analysis however, I keep running into the following error. I tried to solve it by myself however I had no luck ( I tried by removing the exec flag from the files ). I'm using the following sofftware Freesurfer : freesurfer-Linux-centos6_x86_64-dev-20170103-696bbc1 Ubuntu: 14.04.5 LTS WIndows 10 michel@-:~$ recon-all -s bob -hippocampal-subfields-T1 Subject Stamp: freesurfer-Linux-centos6_x86_64-dev-20170103-696bbc1 Current Stamp: freesurfer-Linux-centos6_x86_64-dev-20170103-696bbc1 INFO: SUBJECTS_DIR is /usr/local/freesurfer/subjects Actual FREESURFER_HOME /usr/local/freesurfer -rw-rw-r-- 1 michel 1590 1249629 Jan 24 13:40 /usr/local/freesurfer/subjects/bob/scripts/recon-all.log Linux - 3.4.0+ #1 PREEMPT Thu Aug 1 17:06:05 CST 2013 x86_64 x86_64 x86_64 GNU/Linux '/usr/local/freesurfer/bin/recon-all' -> '/usr/local/freesurfer/subjects/bob/scripts/recon-all.local-copy' #-------------------------------------------- #@# Hippocampal Subfields processing (T1 only) left Tue Jan 24 13:43:46 STD 2017 /usr/local/freesurfer/bin/segmentSF_T1.sh /usr/local/freesurfer/MCRv80 /usr/local/freesurfer bob /usr/local/freesurfer/subjects left See log file: /usr/local/freesurfer/subjects/bob/scripts/hippocampal-subfields-T1.log ------------------------------------------ Setting up environment variables --- LD_LIBRARY_PATH is .:/usr/local/freesurfer/MCRv80/runtime/glnxa64:/usr/local/freesurfer/MCRv80/bin/glnxa64:/usr/local/freesurfer/MCRv80/sys/os/glnxa64:/usr/local/freesurfer/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/usr/local/freesurfer/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/server:/usr/local/freesurfer/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/client:/usr/local/freesurfer/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64: /usr/local/freesurfer/bin/segmentSubjectT1_autoEstimateAlveusML: error while loading shared libraries: libut.so: cannot enable executable stack as shared object requires: Invalid argument #-------------------------------------------- #@# Hippocampal Subfields processing (T1 only) right Tue Jan 24 13:43:46 STD 2017 /usr/local/freesurfer/bin/segmentSF_T1.sh /usr/local/freesurfer/MCRv80 /usr/local/freesurfer bob /usr/local/freesurfer/subjects right See log file: /usr/local/freesurfer/subjects/bob/scripts/hippocampal-subfields-T1.log ------------------------------------------ Setting up environment variables --- LD_LIBRARY_PATH is .:/usr/local/freesurfer/MCRv80/runtime/glnxa64:/usr/local/freesurfer/MCRv80/bin/glnxa64:/usr/local/freesurfer/MCRv80/sys/os/glnxa64:/usr/local/freesurfer/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/usr/local/freesurfer/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/server:/usr/local/freesurfer/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/client:/usr/local/freesurfer/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64: /usr/local/freesurfer/bin/segmentSubjectT1_autoEstimateAlveusML: error while loading shared libraries: libut.so: cannot enable executable stack as shared object requires: Invalid argument Started at Tue Jan 24 13:43:45 STD 2017 Ended at Tue Jan 24 13:43:47 STD 2017 #@#%# recon-all-run-time-hours 0.001 recon-all -s bob finished without error at Tue Jan 24 13:43:47 STD 2017 done Sincerely, Michel

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