Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30088 discussions

Re: [Freesurfer] c_ras for HCP compatibility
by Glasser, Matthew 13 Sep '19

13 Sep '19

External Email - Use Caution Were the images acquired with the animal in a funny position relative to humans? That might be the issue. I would convert DICOMs to NIFTI prior to FreeSurfer, make sure the image is oriented as RPI or LPI and that the labels match the brain (e.g. in a tool like FSLView) and then run FreeSurfer. Matt. From: <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Robert Austin Bruce Benn <robertaustinbruce.benn(a)cnic.es> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Date: Friday, September 13, 2019 at 7:06 AM To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] c_ras for HCP compatibility External Email - Use Caution Hi Y’all, I was wondering if Y’all could tell me how c_ras is calculated in the x_form matrix for orig.mgz? I’ve been using some animal brains, and the pipeline works very well at creating surfaces and aligning them to their coresponding image for freeview. Post pipeline I’ve been applying the cras matix as derived from the orig.mgz to remove the offset for use in wb_view. The commands for applying the transforms work fine. However I end up getting a surface that is either inverted, or perpendicular to the nifti volume in wb_view. The animal image does have a large field of view, with a relatively small brain. I think the cras matrix isn’t getting calculated correctly, but that the images I’m using may not have a standered cras so I may need to hack around that. Could you explain to me how c_ras is calculated? Also if I need to edit c_ras how would I go about doing it? is it derived from the q and s forms? thanks! austin ________________________________ *************** AVISO LEGAL *************** Este mensaje va dirigido, de manera exclusiva, a su destinatario y contiene información confidencial y sujeta al secreto profesional, cuya divulgación no está permitida por la ley. En caso de haber recibido este mensaje por error, le rogamos que, de forma inmediata, nos lo comunique mediante correo electrónico remitido a nuestra atención o a través del teléfono (+34 914531200) y proceda a su eliminación, así como a la de cualquier documento adjunto al mismo. Asimismo, le comunicamos que la distribución, copia o utilización de este mensaje, o de cualquier documento adjunto al mismo, cualquiera que fuera su finalidad, están prohibidas por la ley. Le informamos, como destinatario de este mensaje, que el correo electrónico y las comunicaciones por medio de Internet no permiten asegurar ni garantizar la confidencialidad de los mensajes transmitidos, así como tampoco su integridad o su correcta recepción, por lo que el CNIC no asume responsabilidad alguna por tales circunstancias. Si no consintiese la utilización del correo electrónico o de las comunicaciones vía Internet le rogamos nos lo comunique y ponga en nuestro conocimiento de manera inmediata. ________________________________ *************** LEGAL NOTICE ************** This message is intended exclusively for the person to whom it is addressed and contains privileged and confidential information protected from disclosure by law. If you are not the addressee indicated in this message, you should immediately delete it and any attachments and notify the sender by reply e-mail or by phone (+34 914531200). In such case, you are hereby notified that any dissemination, distribution, copying or use of this message or any attachments, for any purpose, is strictly prohibited by law. We hereby inform you, as addressee of this message, that e-mail and Internet do not guarantee the confidentiality, nor the completeness or proper reception of the messages sent and, thus, CNIC does not assume any liability for those circumstances. Should you not agree to the use of e-mail or to communications via Internet, you are kindly requested to notify us immediately. ________________________________ 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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recon-al- -make all ERRORS
by Alexopoulos, Dimitrios 13 Sep '19

13 Sep '19

External Email - Use Caution Hi, We ran a 2yo subject successfully through FS6.0 with no errors using recon-all -all. We then made some edits to the brainmask.mgz and added controls points and reran the pipeline using: recon-all -make all -s subjectID The rerun failed with error. The log fie is attached. Can someone troubleshoot as to why it failed? Thank. Jim ________________________________ 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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timewindow parameter in mkanalysis-sess
by Caspar M. Schwiedrzik 13 Sep '19

13 Sep '19

External Email - Use Caution Hi! I am having difficulties setting the timewindow parameter in mkanalysis-sess in Freesurfer v5.3. I am trying to use 80 (data acquired with MION), but the parameter does not seem to affect analysis.info, where it is always 40. Is it possible to force a different timewindow? Below is some info from analysis.info. Thanks, Caspar # FSBUILD freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 # MKAVERSION $Id: mkanalysis-sess,v 1.64.2.5 2013/01/22 21:52:07 greve Exp $ # MKACMD /neuro_tools/freesurfer/fsfast/bin/mkanalysis-sess -fsd bold -native -timeoffset -2/2 -event-related -paradigm xxxx.para -nconditions 4 -TR 2 -gammafit 0 8 -gammaexp 0.3 *-timewindow 80* -refeventdur 0.5 -polyfit 2 -hpf 0.0109 -analysis xxxx -funcstem xxxx -runlistfile xxxx.list -nuisreg motion.dat 6 -tpef tpef.dat -acfbins 14 -acffwhm 0 -mask xxxx -force analysis xxxx mcstem fmc funcstem xxxx fsd bold runlistfile xxxx.list TR 2 RegDOF 6 PerSession 1 RawSpace volume native mask xxxx RawFWHM 0 RawSTC none UseB0DC 0 ApplySubCortMask 1 inorm 100 acfbins 14 fixacf 1 acffwhm 0 acfsvd 0 designtype event-related tpexclude tpef.dat nskip 0 polyfit 2 HPFCutoffHz 0.0109 HeteroGCor 0 nconditions 4 parname xxxx.para RefEventDur 0.5 *timewindow 40.000000* prestim 0 TER 0.050000 gamma 0 8 0.3 0 stimulusdelay -2/2 Condition 1 Condition01 Condition 2 Condition02 Condition 3 Condition03 Condition 4 Condition04 nuisreg motion.dat 6

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multiple comparisons correction for brain-behaviour correlations
by Annelies Vant Westeinde 13 Sep '19

13 Sep '19

External Email - Use Caution Dear members, I have run several analyses in which we correlate cognitive performance with vertex-wise cortical surface area, thickness and volume. We ran monte carlo simulation for each correlation. However, we would like to correct the outcome for the number of associations we did, that is for the for 10 different cognitive scales that we tested. How can this be done? We would rather not use bonferroni correction, as it is so strict, but would prefer fdr. Do we need to somehow get the p-values of the cluster peaks that correlated with the cognitive scales and do FDR on those? Or should we adjust the monte carlo simulation threshold to account for the 10 different tests? Thank you in advance, Annelies Annelies van't Westeinde | PHD Candidate Department of Women's and Children's Health | Karolinska Institutet 171 77 Solna | Karolinskavägen 37A +46 760967499 annelies.vant.westeinde(a)ki.se | ki.se<http://ki.se/en/startpage> ______________________________________ Karolinska Institutet – a medical university När du skickar e-post till Karolinska Institutet (KI) innebär detta att KI kommer att behandla dina personuppgifter. Här finns information om hur KI behandlar personuppgifter<https://ki.se/medarbetare/integritetsskyddspolicy>. Sending email to Karolinska Institutet (KI) will result in KI processing your personal data. You can read more about KI’s processing of personal data here<https://ki.se/en/staff/data-protection-policy>.

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Re: [Freesurfer] Hippocampal-subfields-T1 interruption (Bruce Fischl)
by 3 6 13 Sep '19

13 Sep '19

External Email - Use Caution Hi Bruce, I checked the alias, I really aliased mv to “mv -i”, and it worked automatically, after I unaliased. Thanks for your help. Best regards, Guodong > 在 2019年9月13日，上午12:00，freesurfer-request@nmr.mgh.harvard.edu 写道： > > Re: Hippocampal-subfields-T1 interruption (Bruce Fischl)

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c_ras for HCP compatibility
by Robert Austin Bruce Benn 13 Sep '19

13 Sep '19

External Email - Use Caution Hi Y’all, I was wondering if Y’all could tell me how c_ras is calculated in the x_form matrix for orig.mgz? I’ve been using some animal brains, and the pipeline works very well at creating surfaces and aligning them to their coresponding image for freeview. Post pipeline I’ve been applying the cras matix as derived from the orig.mgz to remove the offset for use in wb_view. The commands for applying the transforms work fine. However I end up getting a surface that is either inverted, or perpendicular to the nifti volume in wb_view. The animal image does have a large field of view, with a relatively small brain. I think the cras matrix isn’t getting calculated correctly, but that the images I’m using may not have a standered cras so I may need to hack around that. Could you explain to me how c_ras is calculated? Also if I need to edit c_ras how would I go about doing it? is it derived from the q and s forms? thanks! austin *************** AVISO LEGAL *************** Este mensaje va dirigido, de manera exclusiva, a su destinatario y contiene información confidencial y sujeta al secreto profesional, cuya divulgación no está permitida por la ley. En caso de haber recibido este mensaje por error, le rogamos que, de forma inmediata, nos lo comunique mediante correo electrónico remitido a nuestra atención o a través del teléfono (+34 914531200) y proceda a su eliminación, así como a la de cualquier documento adjunto al mismo. Asimismo, le comunicamos que la distribución, copia o utilización de este mensaje, o de cualquier documento adjunto al mismo, cualquiera que fuera su finalidad, están prohibidas por la ley. Le informamos, como destinatario de este mensaje, que el correo electrónico y las comunicaciones por medio de Internet no permiten asegurar ni garantizar la confidencialidad de los mensajes transmitidos, así como tampoco su integridad o su correcta recepción, por lo que el CNIC no asume responsabilidad alguna por tales circunstancias. Si no consintiese la utilización del correo electrónico o de las comunicaciones vía Internet le rogamos nos lo comunique y ponga en nuestro conocimiento de manera inmediata. *************** LEGAL NOTICE ************** This message is intended exclusively for the person to whom it is addressed and contains privileged and confidential information protected from disclosure by law. If you are not the addressee indicated in this message, you should immediately delete it and any attachments and notify the sender by reply e-mail or by phone (+34 914531200). In such case, you are hereby notified that any dissemination, distribution, copying or use of this message or any attachments, for any purpose, is strictly prohibited by law. We hereby inform you, as addressee of this message, that e-mail and Internet do not guarantee the confidentiality, nor the completeness or proper reception of the messages sent and, thus, CNIC does not assume any liability for those circumstances. Should you not agree to the use of e-mail or to communications via Internet, you are kindly requested to notify us immediately.

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Hippocampal-subfields-T1 interruption
by 3 6 12 Sep '19

12 Sep '19

External Email - Use Caution Hello FreeSurfer Developers, I'm attempting to analyze hippocampal subfields for T1 scan, but when I run the command recon-all -s subjects -hippocampal-subfields-T1, I always get interrupted by the warning : mv: overwrite ‘imageDump.mgz’? It keep running only when I type Y or N. I've searched the list and no similar request have been submitted. Does anyone have any thoughts on how to make it automatically running? Also, I’ve attached the hippocampal-subfields-T1.log in case it's of any use. 1) FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0 2) Platform: CentOS release 7 3) recon-all.log: see attached Best regards, Guodong

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Command failed in QDEC
by James Karantonis 11 Sep '19

11 Sep '19

External Email - Use Caution Hi there, In QDEC, I have successfully imported my data tables, generated stats, and when I go to analyse, I get the following error: “Error in Analyze: command failed mri_glmfit –y…”. It seems this error only occurs when I use the two variables of age and ICV. Whenever I remove one of those variables, or add any additional variables, it appears to work. Specifically, this is for two comparisons, between bipolar patients and healthy controls, bipolar and schizophrenia patients, but it works for schizophrenia and healthy control comparisons. I’m working on an iMac running High Sierra and Freesurfer v.6. Any information on how to resolve this error would be greatly appreciated! I’ve attached a screenshot for reference. Kind regards, James

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neuroimaging postdoc position available
by Keith Schneider 11 Sep '19

11 Sep '19

External Email - Use Caution A post-doctoral position is available with Keith Schneider at the University of Delaware http://keith.psych.udel.edu <http://keith.psych.udel.edu/>. The position is funded by NEI/NIH to study the subcortical mechanisms of vision, audition, attention and dyslexia. The successful candidate will join a thriving neuroimaging community at the University of Delaware. The Center for Biomedical & Brain Imaging includes a Siemens Prisma 3T MRI scanner, simultaneous EEG, TMS, eye-tracking, and a Bruker 9.4 T scanner for small animals. I am looking for a scientist who: * has experience with fMRI * has programming experience (e.g. Matlab or Python) * has an interest in attention, sensory systems, reading and/or neuroimaging methods development (acquisition or analysis) This position is initially for one year but can be renewed as mutually agreed. The start date is flexible but can begin immediately. To inquire, e-mail your CV and a PDF of a first-authored journal article to keithas(a)udel.edu. The University of Delaware is located in Newark, Delaware, a small college town, located along the Northeast Corridor, within 2 hours of New York and Washington, DC, and within an hour of Philadelphia and Baltimore. ----- Keith Schneider Director, Center for Biomedical & Brain Imaging Associate Professor, Department of Psychological & Brain Sciences University of Delaware

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Re: [Freesurfer] Additional scans in hippocampal subfields segmentation
by Rovai Antonin 11 Sep '19

11 Sep '19

External Email - Use Caution I’m resending this request as I really would like to know what you think :-) Best Antonin Hôpital Erasme - ULB Cliniques universitaires de Bruxelles Route de Lennik 808 - B - 1070 Bruxelles S www.erasme.ulb.ac.be Disclaimer : http://www.erasme.ulb.ac.be/email-disclaimer > On 30 Aug 2019, at 11:00, Rovai Antonin <Antonin.Rovai(a)erasme.ulb.ac.be> wrote: > > Hello > > I’d like to know if there is any advantage in having a T2 FLAIR as additional scan (in addition to our 1mm isotropic T1 scans) when using the hippocampal subfield segmentation tool. We do not have T2 nor PD available. > > Thanks for you help > > Antonin Rovai

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