Freesurfer August 2022

freesurfer@nmr.mgh.harvard.edu

85 participants
120 discussions

postdoc
by Thomas Yeo 03 Aug '22

03 Aug '22

External Email - Use Caution Hi Everyone, I am looking for a postdoc to start this year or 2023. Candidates should have a PhD in neuroscience, machine learning or related fields. Research topics are quite flexible and can include can include developing machine learning algorithms for predicting disease progression from large-scale brain imaging data, individual-specific brain network organization, multi-modal fusion/prediction (e.g., relating brain imaging with wearable & smartphone data), neural mass modeling, deep phenotyping, brain network dynamics and naturalistic paradigms. I am particularly interested in applications to aging, Alzheimer’s disease dementia and neurodevelopment. Lab website can be found here (https://secure-web.cisco.com/163_oJDbnYF8kJLTi8C6K0GEnoNtFGd19DY-CEBe1pYtwK…) Interested candidates can email their CV to me. Thanks, Thomas

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Surface-based functional ROI analysis on both hemispheres at once
by Andy Kim 03 Aug '22

03 Aug '22

External Email - Use Caution Dear FreeSurfer Team, Hi. I am writing this email to ask if there is any way to do functional ROI analysis on the both hemispheres at the same time, but not separately. My research question is to investigate visual hierarchy system under certain fMRI tasks using surface-based analysis. I am not interested in differences between hemispheres. There was the same question previously (https://secure-web.cisco.com/1JFM2A4prS9i4P3MGZiI1ScaCdFi7AFRFt2tlUzGfYgNkr…<https://secure-web.cisco.com/1n5iUWdnTAoX8uAScZjw9vgkzDWKHItczK2oXOxDKgvBSj…>) but the answer didn't help. What I understood from the post was that I could do ROI analysis on both hemispheres just like I did it on one hemisphere. So, I tried functional ROI analysis using labels from the both hemisphere (e.g., whole brain V1, not left hemisphere V1). I hypothesized that the results of ROI analyses with left hemisphere and right hemisphere would be the same If it really works. On the other hand, it produced errors and I even couldn't compare the results. Here is what I tried: # merge lh and rh labels mri_mergelabels -i lh.wang2015atlas.V1d.label -i lh.wang2015atlas.V1v.label -i lh.wang2015atlas.V2d.label -i lh.wang2015atlas.V2v.label -i rh.wang2015atlas.V1d.label -i rh.wang2015atlas.V1v.label -i rh.wang2015atlas.V2d.label -i rh.wang2015atlas.V2v.label -o lhrh.wang2015atlas.V1d+v+V2d+v.label # GL is the project name. funcroi-config -label lhrh.wang2015atlas.V1d+v+V2d+v.label -analysis GLanalysis.rh -roi rhlh.wang2015atlas.V1d+v+V2d+v.roicfg funcroi-sess -sf GLsublist -roi rhlh.wang2015atlas.V1d+v+V2d+v.roicfg funcroi-table-sess command showed an error "ERROR: there is a vertex in the label that cannot be matched to the surface. This usually occurs when the label and surface are from different subjects or hemispheres or the surface has been changed since the label was created." The command showed no error with -anlysis GLanlaysis.lh option. Still, it looked a bit weird as you can see the attached file. The attached files are the output from funcroi-sess with different hemispheres options. What should I do for doing ROI analysis from the both hemispheres at once? If I can't, would it be good idea that I get mean beta values from each hemisphere, add them together and divide by 2 to get the average beta value? Kind Regards, Andy (Junghyun) Kim

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segment_subregions error
by Sanchez, Juan (NYSPI) 03 Aug '22

03 Aug '22

External Email - Use Caution I am running segment_subregions 7.3 on abcd-hcp freesurfer output docker and got the following error: Step 2: aligning atlas to reference segmentation Traceback (most recent call last): File "/usr/local/freesurfer/7.3.0-1/python/scripts/segment_subregions", line 99, in <module> subregions.run_cross_sectional(args.structure, parameters) File "/usr/local/freesurfer/7.3.0-1/python/packages/freesurfer/subregions/process.py", line 52, in run_cross_sectional model.align_atlas_to_seg() File "/usr/local/freesurfer/7.3.0-1/python/packages/freesurfer/subregions/core.py", line 240, in align_atlas_to_seg mask = mask.resize(1, interp='nearest') TypeError: resize() got an unexpected keyword argument 'interp'

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Post-doctoral position at University of Pittsburgh in population neuroscience
by James Hengenius 03 Aug '22

03 Aug '22

External Email - Use Caution *Dear All, please see the opportunity for a Post-Doctoral Associate position:* *Link to apply*: Job Description - Post Doctoral Associate (ROSANO) (21008433) (taleo.net) <https://secure-web.cisco.com/1Wrh34ETeGvc-jjA4jE946BZQm4ltxhurWKS1h34wjCz6p…> https://secure-web.cisco.com/1ZOanogXZkLzkQnqrC_mxzi3jWIx4w7dKQBsNZA5Sfk_8P… <https://secure-web.cisco.com/1USBso__-_R27IqS5zYk37Cy_hgY1bIoQg3C4KLoxnGalC…> position # 21008433 *Post-Doctoral Associate* (with Dr. Caterina Rosano) GSPH-Epidemiology - Pennsylvania-Pittsburgh - (21008433) Post-Doctoral Associate; Graduate School of Public Health (GSPH), Department of Epidemiology The Postdoctoral Associate will join a cross-institutional research team focused on the intersection of epidemiology, neuroscience, neuroimaging, causal inference, and machine learning. The Postdoctoral Associate is expected to take a leadership role in ongoing research projects, including developing novel and important research questions, analyzing data, writing manuscripts, and meeting with mentors. The candidate will be encouraged to develop their own personal goals within the context of the existing research program, and will work with mentors to achieve these goals. *Duties and responsibilities*: All activities below will be performed independently and then reviewed by the mentors for discussion and revisions. -Develop short-term (6 months) and longer-term (1-2 years) career goals. -Develop important and novel research questions within the context of the research program. -Analyze neuroimaging and epidemiological data -Interpret results. -Write manuscripts based on research findings. -Provide some mentorship to Ph.D. students and contribute to their manuscripts as appropriate. *Expectations: *The Postdoctoral Associate will have a Ph.D. in epidemiology, biostatistics, neuroscience, or another area of public health. They will also have experience in causal inference and/or machine learning. The Postdoctoral Associate is expected to produce 3 to 4 first-authored papers per year and co-author manuscripts that come out of the research group, as appropriate, as well as submit one or more abstracts to scientific meetings each year. They will attend weekly mentorship meetings and biweekly research team meetings, and provide input on other work coming out of the research group. *Opportunities:* Attendance of several annual meetings, including the society of neuroscience, Human Brain Mapping, Gerontological Society of America. Presentation of results in those scientific meetings, to the Epidemiology Department, to visiting experts, and to our research team; Participation in career development activities through the department, school, and university, including those at the Office of Academic Career Development that are available virtually; Development of research ideas suitable for funding, including a career development award (K01 or K99/R00), depending on the Postdoctoral Associate's interest and goals. Please attach a cover letter, current CV, statement of research interests (1-2 page max) and contact information for three references to your Talent Center application. The University of Pittsburgh is an Affirmative Action/Equal Opportunity Employer and values equality of opportunity, human dignity and diversity. EOE, including disability/vets Assignment Category Full-time regular, Campus Pittsburgh, Required Attachments Cover Letter, Curriculum Vitae Job Description - Post Doctoral Associate (ROSANO) (21008433) (taleo.net) <https://secure-web.cisco.com/1Wrh34ETeGvc-jjA4jE946BZQm4ltxhurWKS1h34wjCz6p…> https://secure-web.cisco.com/1ZOanogXZkLzkQnqrC_mxzi3jWIx4w7dKQBsNZA5Sfk_8P… <https://secure-web.cisco.com/1USBso__-_R27IqS5zYk37Cy_hgY1bIoQg3C4KLoxnGalC…> position # 21008433

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Inquiry about infant freesurfer pipeline - wm segmentation options
by Shinwon Park 02 Aug '22

02 Aug '22

External Email - Use Caution Dear Experts, We ran the freesurfer infant pipeline on our dataset consisting of 1 and 2 year olds, and noticed that the white matter segmentation does not perform well. Specifically, it does not extend all the way up to the lateral regions of the brain. Is there a way to modify some options to increase white matter segmentation coverage? For instance, in the adult freesurfer pipeline using the *mri_segment *command we can adjust the white matter low and high limits using the -wm_low and -wm_high flags, respectively. Looking through the commands of the freesurfer infant pipeline, the " *mri_label_fusion*" function which is called upon in the *run_label_fusion.sh* along with several other commands such as " *mri_correct_segmentations*" seems to play a key role in the segmentation process. However, we could not find any usage documentation for these commands. We would greatly appreciate If you could share the usage descriptions for the commands used in the freesurfer infant pipeline! Best, Shinwon Park

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Moving out of mailing list
by gianrocco 02 Aug '22

02 Aug '22

External Email - Use Caution Dear @admins, Did you think about using something more modern than a mailing list? A tool like https://secure-web.cisco.com/14svoEZ7j0oVc1meYwLtCoNc_ET_uCBHb1gIzmf5gM89N6… <https://secure-web.cisco.com/14svoEZ7j0oVc1meYwLtCoNc_ET_uCBHb1gIzmf5gM89N6…> for instance ? Kind regards, Gianrocco Lazzari, PhD Data Scientist Bottneuro AG Novartis Campus Lichtstrasse 35 CH-4056 Basel http://secure-web.cisco.com/1Jkvm-7Gx7Ts37DnGItKY2lqsuIFF33OmReEFZ_jL5mErKQ…

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Tracula error in path construction
by Shanika Jayakody 01 Aug '22

01 Aug '22

External Email - Use Caution Dear Anastasia I am running tracula on FreeSurfer 7.2. It worked fine on a linux computer now I am changing to a Cloud workstation. Attached is my Configuration file. For this person the pipeline worked without errors until path reconstruction but exists saying the following I have checked my bvecs and bvals in the subjects directory and also in dmri Any suggestion for me to try would be great-thanks so much! I tried to attach the trac-all log file but then the email is too big to be posted. Oshadi Loading DWIs from /gs/gsfs0/users/helena_blumen_lab/TRACULA//30018/dmri/data.nii.gz Loading mask from /gs/gsfs0/users/helena_blumen_lab/TRACULA//30018/dlabel/diff/aparc+aseg_mask.bbr.nii.gz Loading BEDPOST parameter samples from /gs/gsfs0/users/helena_blumen_lab/TRACULA//30018/dmri.bedpostX Killed Linux sjayakody 4.18.0-348.el8.x86_64 #1 SMP Mon Oct 4 12:17:22 EDT 2021 x86_64 x86_64 x86_64 GNU/Linux

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The password request for the Freesurfer VirtualBox Image
by Nina Omejc 01 Aug '22

01 Aug '22

External Email - Use Caution Hi, My name is Nina and I'm a PhD Student from Department of Knowledge technologies At Jožef Stefan Institute, Ljubljana. I downloaded " Freesurfer VirtualBox Image" and I need the paswword to login as the user "developer" in the login menu. Thank you. Best regards, Nina

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TRACULA in FreeSurfer version 7.3
by kingwai.chu＠gmail.com 01 Aug '22

01 Aug '22

External Email - Use Caution Hi Anastasia, � Just downloaded FreeSurfer version 7.3 and trying out TRACULA. Ran recon-all, segmentThalamicNuclei.sh, and trac-all in v7.3 However trac-all -prep is looking for ThalamicNuclei.v12.T1.FSvoxelSpace.mgz from segmentThalamicNuclei.sh which doesn’t exist. Because in v7.3, segmentThalamicNuclei.sh output a new version v13 (ThalamicNuclei.v13.T1.FSvoxelSpace.mgz). I worked around this problem by linking ThalamicNuclei.v12.T1.FSvoxelSpace.mgz to ThalamicNuclei.v13.T1.FSvoxelSpace.mgz ln -s ThalamicNuclei.v13.T1.FSvoxelSpace.mgz ThalamicNuclei.v12.T1.FSvoxelSpace.mgz � trac-all finished w/o problem. � trac-all -version trac-all 7.3.0 � I seems trac-all in v7.3 forgets to update the fact that segmentThalamicNuclei.sh output v13 of the file. Or it is looking for v12 for a reason? � Is my fix correct? � Thanks, � King-Wai

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Re: [Freesurfer] TRACULA in FreeSurfer version 7.3
by fsbuild 01 Aug '22

01 Aug '22

External Email - Use Caution There is a change related to that, Date:   Mon Jul 25 21:24:30 2022 -0400     trac-preproc. #BF. Changed expected thalseg version to 1.3; also added an option to be able to spec the thalseg file. AY should look at it. - in the latest development builds, which are located under,https://secure-web.cisco.com/16IqsFJkXTetOby5z7oQ2GGW3ceVlc5mNqOcsSHL… That and some other changes will make it into the 7.3.2 release. - R. On Aug 1, 2022, at 00:44, kingwai.chu(a)gmail.com wrote:        External Email - Use Caution        Hi Anastasia, I thought he wants me to run trac-preproc.sh he sent to run it directly.I wasn’t told to replace it with the one in the original 7.3. After replacing the original one with the modified one Doug sent, trac-all -prep -c config.file runs w/o problem. Thanks, King-Wai From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> On Behalf Of Yendiki, AnastasiaSent: Monday, August 1, 2022 12:15 AMTo: 'Freesurfer support list' <freesurfer@nmr.mgh.harvard.edu>Subject: Re: [Freesurfer] TRACULA in FreeSurfer version 7.3 Indeed. Doug sent you a modified version of trac-preproc, which is a script that's called by trac-all. The idea was for you to overwrite $FREESURFER_HOME/bin/trac-preproc with the version that Doug sent, then run trac-all like before. Did you try that?From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of kingwai.chu@gmail.com<kingwai.chu@gmail.com>Sent: Monday, August 1, 2022 12:10 AMTo: 'Freesurfer support list' <freesurfer@nmr.mgh.harvard.edu>Subject: Re: [Freesurfer] TRACULA in FreeSurfer version 7.3         External Email - Use Caution        Hi Anastasia, The problem is in 7.3, trac-all -prep -c config.file is looking for ThalamicNuclei.v12.T1.FSvoxelSpace.mgz  from segmentThalamicNuclei.sh which doesn’t exist.Because in v7.3, segmentThalamicNuclei.sh output a new version v13 (ThalamicNuclei.v13.T1.FSvoxelSpace.mgz). Thanks, King-Wai From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Yendiki, AnastasiaSent: Monday, August 1, 2022 12:03 AMTo: 'Freesurfer support list' <freesurfer@nmr.mgh.harvard.edu>Subject: Re: [Freesurfer] TRACULA in FreeSurfer version 7.3 Hi King-Wai - You are not supposed to run trac-preproc directly. Run trac-all -c configfile, like before. Anastasia. From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of kingwai.chu@gmail.com<kingwai.chu@gmail.com>Sent: Monday, July 25, 2022 2:11 PMTo: 'Freesurfer support list' <freesurfer@nmr.mgh.harvard.edu>Subject: Re: [Freesurfer] TRACULA in FreeSurfer version 7.3         External Email - Use Caution        Hi Douglas, Thank you for looking into this.It gives the following error. trac-preproc.sh -c config.fileintrareg: Undefined variable. Thanks, King-Wai From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Douglas N.. GreveSent: Monday, July 25, 2022 1:55 PMTo: freesurfer@nmr.mgh.harvard.eduSubject: Re: [Freesurfer] TRACULA in FreeSurfer version 7.3 Can you copy the attached trac-preproc into $FREESURFER/bin and try again (after removing the link)? On 7/22/2022 8:36 AM, kingwai.chu@gmail.com wrote:        External Email - Use Caution        Hi Anastasia, Just downloaded FreeSurfer version 7.3 and trying out TRACULA.Ran recon-all, segmentThalamicNuclei.sh, and trac-all in v7.3However trac-all -prep is looking for ThalamicNuclei.v12.T1.FSvoxelSpace.mgz  from segmentThalamicNuclei.sh which doesn’t exist.Because in v7.3, segmentThalamicNuclei.sh output a new version v13 (ThalamicNuclei.v13.T1.FSvoxelSpace.mgz).I worked around this problem by linking ThalamicNuclei.v12.T1.FSvoxelSpace.mgz  to ThalamicNuclei.v13.T1.FSvoxelSpace.mgzln -s ThalamicNuclei.v13.T1.FSvoxelSpace.mgz ThalamicNuclei.v12.T1.FSvoxelSpace.mgz trac-all finished w/o problem. trac-all -versiontrac-all 7.3.0 I seems trac-all in v7.3 forgets to update the fact that segmentThalamicNuclei.sh output v13 of the file.Or it is looking for v12 for a reason? Is my fix correct? Thanks, King-Wai _______________________________________________Freesurfer mailing listFreesurfer(a)nmr.mgh.harvard.eduMailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1v-b5JJwuDi1SzLbIsac4ppx7Moeb9XlbmcaO28MpjIUuD… mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer On Aug 1, 2022, at 00:14, Yendiki, Anastasia <AYENDIKI(a)mgh.harvard.edu> wrote:Indeed. Doug sent you a modified version of trac-preproc, which is a script that's called by trac-all. The idea was for you to overwrite $FREESURFER_HOME/bin/trac-preproc with the version that Doug sent, then run trac-all like before. Did you try that?From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of kingwai.chu(a)gmail.com <kingwai.chu@gmail.com>Sent: Monday, August 1, 2022 12:10 AMTo: 'Freesurfer support list' <freesurfer@nmr.mgh.harvard.edu>Subject: Re: [Freesurfer] TRACULA in FreeSurfer version 7.3         External Email - Use Caution        Hi Anastasia, The problem is in 7.3, trac-all -prep -c config.file is looking for ThalamicNuclei.v12.T1.FSvoxelSpace.mgz  from segmentThalamicNuclei.sh which doesn’t exist.Because in v7.3, segmentThalamicNuclei.sh output a new version v13 (ThalamicNuclei.v13.T1.FSvoxelSpace.mgz). Thanks, King-Wai From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> On Behalf Of Yendiki, AnastasiaSent: Monday, August 1, 2022 12:03 AMTo: 'Freesurfer support list' <freesurfer@nmr.mgh.harvard.edu>Subject: Re: [Freesurfer] TRACULA in FreeSurfer version 7.3 Hi King-Wai - You are not supposed to run trac-preproc directly. Run trac-all -c configfile, like before. Anastasia. From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of kingwai.chu@gmail.com<kingwai.chu@gmail.com>Sent: Monday, July 25, 2022 2:11 PMTo: 'Freesurfer support list' <freesurfer@nmr.mgh.harvard.edu>Subject: Re: [Freesurfer] TRACULA in FreeSurfer version 7.3         External Email - Use Caution        Hi Douglas, Thank you for looking into this.It gives the following error. trac-preproc.sh -c config.fileintrareg: Undefined variable. Thanks, King-Wai From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Douglas N. GreveSent: Monday, July 25, 2022 1:55 PMTo: freesurfer@nmr.mgh.harvard.eduSubject: Re: [Freesurfer] TRACULA in FreeSurfer version 7.3 Can you copy the attached trac-preproc into $FREESURFER/bin and try again (after removing the link)?On 7/22/2022 8:36 AM, kingwai.chu@gmail.com wrote:        External Email - Use Caution        Hi Anastasia, Just downloaded FreeSurfer version 7.3 and trying out TRACULA.Ran recon-all, segmentThalamicNuclei.sh, and trac-all in v7.3However trac-all -prep is looking for ThalamicNuclei.v12.T1.FSvoxelSpace.mgz  from segmentThalamicNuclei.sh which doesn’t exist.Because in v7.3, segmentThalamicNuclei.sh output a new version v13 (ThalamicNuclei.v13.T1.FSvoxelSpace.mgz).I worked around this problem by linking ThalamicNuclei.v12.T1.FSvoxelSpace.mgz  to ThalamicNuclei.v13.T1.FSvoxelSpace.mgzln -s ThalamicNuclei.v13.T1.FSvoxelSpace.mgz ThalamicNuclei.v12.T1.FSvoxelSpace.mgz trac-all finished w/o problem. trac-all -versiontrac-all 7.3.0 I seems trac-all in v7.3 forgets to update the fact that segmentThalamicNuclei.sh output v13 of the file.Or it is looking for v12 for a reason? Is my fix correct? Thanks, King-Wai _______________________________________________Freesurfer mailing listFreesurfer(a)nmr.mgh.harvard.eduMailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1v-b5JJwuDi1SzLbIsac4ppx7Moeb9XlbmcaO28MpjIUuD… mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Freesurfer August 2022