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Re: [Freesurfer] {Filename?} Hippocampal subfields --> Can't find a *ctf file?
by pierre deman 08 Jul '16

08 Jul '16

Thanks ! Cheers, Pierre On Jul 8, 2016 1:14 PM, "Iglesias, Eugenio" <e.iglesias(a)ucl.ac.uk> wrote: I think I identified the problem; hopefully this will be sorted out very soon. Cheers, Eugenio Juan Eugenio Iglesias Translational Imaging Group University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/ On 7 Jul 2016, at 19:23, Perea Camargo, Rodrigo Dennis < RPEREACAMARGO(a)mgh.harvard.edu> wrote: *Warning: This message has had one or more attachments removed (recon-all.cmd). Please read the "UCL-Attachment-Warning.txt" attachment(s) for more information.* Hi all, I am currently trying to run hippocampal subfields in a couple of my participants using FreeSurfer6.0 (located at *nmr*:/usr/local/freesurfer/stable6). It did run successfully for many of my subjects earlier in the year but some of them only had a let hemisphere segmentation. So I decided to re-run them using launchpad and also my local nmr computer. Now, none of the hippocampal sufields segmentations appear (no rh/lh.hippoSfLabels-T1-T2.*.mgz appears). I looked at <FSSUBJECT>/scripts/scripts/hippocampal-subfields-T1T2.log and the error I get is: Error:Cannot find CTF archive /autofs/cluster/freesurfer/centos6_x86_64/stable6/bin/segmentSubjectT1T2_autoEstimateAlveusML.ctf Could a missing *.ctf cause the error? (btw, the re-run happened after the major hardware crash). Thanks in advance for your help, Rodrigo PS: I am attaching the *log files as suggested in the bug reporting page. --- Rodrigo Dennis Perea Research Fellow Department of Radiology Athinoula A. Martinos Center Massachusetts General Hospital rpereacamargo(a)mgh.harvard.edu This is a message from the E-Mail Virus Protection System at UCL ---------------------------------------------------------------------- The original e-mail attachment (recon-all.cmd) is on the list of unacceptable attachments for UCL and has been replaced by this warning message. This constraint is in place to protect users from viruses and other malware. If you think this attachment is a legitimate file and you wish to receive it, please ask the sender to rename the file extension (eg rename file.exe to file.ex_) and resend it to avoid this constraint. On receiving the file you will have to save it and rename it back to its original extension. Reference: 1bLDxs-0003ZW-3F -- UCL E-mail Virus Protection System Servicedesk(a)ucl.ac.uk Internal phone: 25000 <hippocampal-subfields-T1T2.log><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.

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PhD/Postdoc positions in Neuroscience of Autism/Dyslexia, Max Planck Institute, Leipzig
by Katharina von Kriegstein 08 Jul '16

08 Jul '16

Applications are welcomed for two researcher positions at doctoral or postdoctoral level at the Max Planck Institute for Human Cognitive and Brain Sciences (MPI-CBS) in Leipzig, Germany, in the Neural Mechanisms of Human Communication group led by Katharina von Kriegstein. PhD student or Postdoctoral Position in Neuroscience of Developmental Dyslexia: The objective of the research project is to use functional and structural magnetic resonance imaging (MRI) and behavioural intervention training to understand the role of auditory and visual sensory processing in populations with developmental dyslexia. Further information on the position can be found here: http://www.cbs.mpg.de/489916/job_full_offer_10626437?c=7390 PhD student or Postdoctoral position in Neuroscience of Autism Spectrum Disorder: The objective of the research project is to use high-resolution functional and structural magnetic resonance imaging (MRI) and behavioural tests to understand the role of auditory and visual sensory processing in populations with Autism Spectrum Disorder. Further information on the position can be found here: http://www.cbs.mpg.de/490195/job_full_offer_10626459?c=7390 Both positions are funded by an ERC-Consolidator grant. --- Katharina von Kriegstein Max Planck Research Group Leader Max Planck Institute for Human Cognitive and Brain Sciences Stephanstr. 1A, 04103 Leipzig, Germany Professor of Cognitive and Clinical Neuroscience Humboldt University of Berlin Rudower Chaussee 18, 12489 Berlin, Germany Phone +49 (0) 341-9940-2476 Fax +49 (0) 341-9940-2448 http://www.cbs.mpg.de/independent-research-groups/human-communication

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LGI
by Walid Yassin 07 Jul '16

07 Jul '16

Hello again, Sorry for posting twice, but does someone know what might be the problem? Thank you in advance. I’m trying to run recon-all -lgi - s Subjectname on my data but i am getting this error! ******************************************************* Error in dsearchn (line 79) [d(i),t(i)] = min(sum((x-yi).^2,2)); Error in mesh_vertex_nearest (line 29) nearestIndex = dsearchn(vertices,points); Error in reorganize_verticeslist (line 28) [nextindex,nextvalue]=mesh_vertex_nearest(mesh_total.vertices(remaininglist,:),mesh_total.vertices(verticeslist(start_vertex),:)); Error in make_roi_paths (line 93) reorglist = reorganize_verticeslist (mesh_total, A, mesh_outer, perim, verticeslist, step); >> ERROR: make_roi_paths did not complete successfully! ******************************************************* *I checked the archives and saw a reply by Marie to someone who had the same problem.* *She recommended changing the info inside “SearchProjectionByPial.m" in the ~/Application/freesurfer/matlab directory to:* ******************************************************* function [verticeslist]=SearchProjectionOnPial(mesh_total,mesh_outer,perim, step) % step is typically set between 5 and 10. Default is 7, increasing it will % limit redundancies in the resulting path file. verticeslist=[]; si=max(size(perim)); for t=1:step:si [nearestIndexMT,nearestValuesMT]=mesh_vertex_nearest(mesh_total.vertices,mesh_outer.vertices(perim(t),:)); verticeslist= [verticeslist nearestIndexMT]; end verticeslist=unique(vertices list); ******************************************************* Which i did, but i am still getting this error!* Any recommendations on what to do next? I am running MATLAB_R2016. Thank you in advance, WY

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question about volume of the hippocampus
by kjunji＠med.kanazawa-u.ac.jp 07 Jul '16

07 Jul '16

Dear freesurfer developers. I am working at department of neurology in university Hospital, Japan. I am beginner of freesurfer, please forgive me to ask you a basic question. I want to measure the volume of the hippocampus in my patients. I was able to segment the MRI successfully and display the image in freeviewer. However, I could not recognize the way to obtain the volume of the hippocampus. *I saw the "mail acheive" (http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg14679.html) however, I could not understand the way to look at the the aseg.stats. Could you teach me the way for obtaining the volume of the hippocampus? I and very looking forward to hearing from you. Yours sincerely, Junji Komatsu

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MRI image prepossession for FS
by shi yao wang 07 Jul '16

07 Jul '16

Dear FS experts, I am planning to use FS to analyze large dataset from population. I am wondering if there were software can automatically check T1 imaging quality for FS? such as monitoring head motion, noise, et al. thanks Lawrence Emory

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fslaverage/MNI coordinates
by Li, Baojuan 07 Jul '16

07 Jul '16

Dear Freesurfer experts, I am using MNE (with MEG data) to define my ROIs for a connectivity analysis. I am going through the following steps to get the MNI coordinates of the regions: 1. Morph the subject's brain to fslaverage; 2. Load the inflated surface of fslaverage to MNE analyze; 3. Look for regions that are activated during my task; 3. Use view>show coordinates to show the coordinates of the vertex; 4. The surface RAS (MRI) coordinates are shown; 5. Used these coordinates as MNI coordinates. Because I was using SPM in the past and am quite new to freesurfer, I strongly hope someone can help me to check if I have done it correctly. Thank you so much for your help! Best wishes, Baojuan

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BrainSeg Volume Clarification
by Cook, Bernie 07 Jul '16

07 Jul '16

All, Upon looking at online forums and the FreeSurfer wiki, I have come to the understanding that "BrainSeg" volume in the aseg.stats file includes all cortical and subcortical gray matter, cerebellar gray matter; cortical, subcortical and cerebellar white matter and white matter hypointensities; and all ventricle volumes, but excludes the brain stem. When using the aseg.stats file for included subject "bert" to check my understanding of which volumes are used, I cannot seem to produce identical "BrainSegVol-to-TIV" ratios. I am adding the following volumes, all in mm^3, to obtain the brain volume: TotalGrayVol: 658087.056198 CorticalWhiteMatterVol: 485627.161537 Left-Lateral-Ventricle: 6562.6 Left-Inf-Lat-Vent: 228.3 Left-Cerebellum-White-Matter: 15708.2 3rd-Ventricle: 997.5 4th Ventricle: 1714.2 Right-Lateral-Ventricle: 6039.9 Right-Inf-Lat-Vent: 160.3 Right-Cerebellum-White-Matter: 15694.5 5th-Ventricle: 14.1 WM-hypointensities: 1002.6 Sum of individual measures: 1191836.418 Output of BrainSegVol: 1193318 And when normalizing the subject's brain volume by the eTIV measure (1594882.911364), I obtain the following: Individual measures: 0.7473 BrainSegVol-to-eTIV: 0.7482 Is there a reason that these two measurements are slightly off? I'm wondering whether there's certain volumes used for BrainSegVol that I missed, or ones that I included that would not be present in the output. Moreover, I'm wondering whether this could potentially be a result of using surface volumes (BrainSegVol) versus using both surface and voxel-space calculations (my addition method). Any help is appreciated. Thank you in advance. Best, [1455168447449_PastedImage] Bernard L. Cook Biomedical Engineering | Class of 2017 BMES at Ohio State | Professional Development Chair '16-'17 IBRC | Undergraduate Research Assistant 440-623-4710 cook.1327(a)osu.edu<mailto:cook.1327@osu.edu>

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continuity in volumes converted from labels
by MIKHAEL Shadia 07 Jul '16

07 Jul '16

Hello, I am interested in the cortical parcellations at the pial (grey matter) and white matter layers I have extracted grey matter (pial) and white matter (white) labels for a gyrus (right superior frontal gyrus, label 2028) mri_annotation2label --subject s1/12copy --hemi rh --labelbase ./12copy/label/rh.cortex --surface pial mri_annotation2label --subject s1/12copy --hemi rh --labelbase ./12copy/label/rh.cortex --surface white then converted the above 2 files (renamed to ...-wm and ...-gm) for the superior frontal gyrus to nifti's for viewing in other applications mri_label2vol --label ./label/rh.cortex-028.label --o rh-cortex-028-rsfg-wm.nii --identity --temp ./mri/T1.mgz mri_label2vol --label ./label/rh.cortex-028.label --o rh-cortex-028-rsfg-gm.nii --identity --temp ./mri/T1.mgz My goal is to run some statistics on 2 nifti's, which requires continuity in the nonzero voxels, in at least 1 of the 3 directions (x/y/z). This isn't the case for this gyri, particularly at the pial layer (shown in blue in the attachment). Is there a way in which this could be achieved? Have I missed any steps? Many thanks in advance. Shads The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

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Design Matrix Creation
by Timothy Hendrickson 07 Jul '16

07 Jul '16

Hi Doug, I just wanted to make sure that we were on the same page. I may have been a little unclear in what I would ideally like to do. For #2 what I would like to do is take into account age slopes and total intracranial slopes for gender, and age slopes and total intracranial slopes for diagnosis. I was not implying that I wanted diagnosis and gender to interact. Assuming that you understood this previously could you please explain why you would model the matrix this way? I do not fully understand. Respectfully, -Tim >I did not get the same matrix. Here's how I would do it >Columns 1-16 model the intercepts for all your classes >Columns 17-20 model the ages for your gender-x-diagnosis subclasses >Columns 21-24 model the ICV for your gender-x-diagnosis subclasses On 07/06/2016 02:04 PM, Timothy Hendrickson wrote: > Freesurfer Support, > > Thank you for your support with my previous line of questions regarding > design matrix creation. > I have manually created another design matrix and want to ensure that I > designed it correctly. > > An example of my FSGD file is as follows below: > Class SITE 1-Male-Control > Class SITE 1-Male-PATIENT > Class SITE 1-Female-Control > Class SITE 1-Female-PATIENT > Class SITE 2-Male-Control > Class SITE 2-Male-PATIENT > Class SITE 2-Female-Control > Class SITE 2-Female-PATIENT > Class SITE 3-Male-Control > Class SITE 3-Male-PATIENT > Class SITE 3-Female-Control > Class SITE 3-Female-PATIENT > Class SITE 4-Male-Control > Class SITE 4-Male-PATIENT > Class SITE 4-Female-Control > Class SITE 4-Female-PATIENT > Variables age_at_scan total_intracranial_volume > study site levels = 1, 2, 3, 4 > gender levels = Male, Female > diagnosis levels = PATIENT, Control > age_at_scan = covariate age > total_intracranial_volume = covariate total intracranial volume > > What I would ideally like to do is: > > 1) Take into account offset differences amongst diagnosis, gender, and study > site. > > 2) Allowing a difference in age slope, and total intracranial volume slope > amongst the diagnosis and gender levels. > > 3) Modeling the age slope and total intracranial volume slope as the same for > the study site levels. > Let's image that the first participant is from site 1, Male, and control, and > is 12 and has a TIV of 30,000. > The second participant is from site 2, Female, and PATIENT, and is 14, and > has a TIV of 25,000. > My understanding of the design matrix would be as follows: > 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 12 0 0 0 30000 0 0 0 > 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 14 0 0 0 25000 > -Tim > > >Yes, create your matrix manually. > > > >Those matrix lines are not quite right. The ages are in the correct > >column, but you need a 1 somewhere in columns 1-8 to indicate the class > >(ie, site/dx) that the subject is in. > On 05/26/2016 12:57 PM, Timothy Hendrickson wrote: > > Hi Doug, > > > > Thank you for such a prompt response. Just to be clear you are > > recommending that I manually create the matrix file right? > > > > If so I want to ensure that I am understanding how to design the > > matrix file properly. > > > > Let's imagine that the first participant is a control and is 13 and > > the second is a patient and is 15. My understanding is that the matrix > > file would be as follows: > > 0 0 0 0 0 0 0 0 13 0 > > 0 0 0 0 0 0 0 0 0 15. > > > > -Tim > > Previous correspondences are below: > > > > You'll need a regressor for each of the 8 classes you describe below. > > You can use mri_glmfit to generate this (Xg.dat file) > > You'll need two more regressors for age, one for each diagnosis. If a > > subject (ie, row) is a control then the two values will be AGE 0. If the > > subject of the row is a patient, then the two values will be 0 AGE. You > > can then set up a Controls-Patients age (ie, interaction between dx and > > age) contrast like > > [0 0 0 0 0 0 0 0 1 -1] > > On 05/24/2016 02:30 PM, Timothy Hendrickson wrote: > > > > > > Freesurfer Support, > > > > > > I'd like to create a design matrix for a group analysis outside of the > > > DODS and DOSS models. I understand that in order to do this the -X > > > flag must be used. However, I have been unable to find examples of how > > > to do this. > > > > > > I am hoping to reveal a difference in thickness or gyrification > > > amongst a clinical population. The data set contains two factors: > > > diagnosis, and study site and one covariate: age. Diagnosis has two > > > levels: controls, and patients. Study site has four levels, one level > > > for each location the data has been collected from. > > > > > > What I would ideally like to do is: > > > > > > 1) Take into account offset differences amongst diagnosis and study site. > > > > > > 2) Allowing a difference in age slope amongst the diagnosis levels > > > > > > 3) Modeling the age slope as the same for the study site levels > > > > > > My FSGD file is designed as follows > > > > > > Class SITE 1-Control > > > Class SITE 1-PATIENT > > > Class SITE 2-Control > > > Class SITE 2-PATIENT > > > Class SITE 3-Control > > > Class SITE 3-PATIENT > > > Class SITE 4-Control > > > Class SITE 4-PATIENT > > > Variables age_at_scan > > > > > > study site levels = 1,2,3 and 4 > > > diagnosis levels = PATIENT and Control > > > age_at_scan = covariate age > > > > > > Any advice would be greatly appreciated. > > > > > > Respectfully, > > > > > > Tim > > > > > > -- > > > Timothy Hendrickson > > > Department of Psychiatry > > > University of Minnesota > > > Mobile: 507-259-3434 <tel:507-259-3434> (texts okay) > >

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mapping a surface from fsaverage_sym to the subject's native surface
by Ali-Reza Mohammadi-Nejad 07 Jul '16

07 Jul '16

Dear Freesurfer experts, Based on the FS wiki, I calculated the cortical thickness difference between the lh and rh of a subject.Now, I want to use the “mris_apply_reg” command to map the “left-right difference” from fsaverage_sym back to the subject's native surface.Unfortunately, I did not find the appropriate options of this command to do this work.Thanks for any help. Best regards,Ali-Reza Ali-Reza Mohammadi-Nejad Pre-doctoral research fellow Radiology and Neurology Research Henry Ford Health System Detroit, MI 48202, USA

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