Freesurfer August 2018

freesurfer@nmr.mgh.harvard.edu

104 participants
167 discussions

long_mris_slopes: error: cannot create a table with longitudinal pc1
by Shatil, Anwar Shahadat 05 Sep '18

05 Sep '18

External Email - Use Caution ?Dear Doug: I am trying to get a table containing pc1 values for each subject in a longitudinal study and failed to extract this. I use the code below: long_mris_slopes --qdec ./qdec/long.qdec.table.2.dat --meas thickness --hemi lh --do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label --time years --qcache fsaverage --sd /Users/richardaviv/Desktop/Longitudinal_FS --out-pc1 out-pc1.dat It says long_mris_slopes: error: no such option: --out-pc1 However in the --help file it says: Within-Subject Output: Pass these to overwrite the default names: --out-avg=OUT_AVG filename to store temporal average in <template>/stats/<OUT_AVG> (default: long.<stats>.<meas>-avg.dat) --out-rate=OUT_RATE filename to store rate in <template>/stats/<OUT_RATE> (default: long.<stats>.<meas>-rate.dat) --out-pc1fit=OUT_PC1FIT filename to store pct. change (to tp1fit) in <template>/stats/<OUT_PC1FIT> (default: long.<stats>.<meas>-pc1fit.dat) --out-pc1=OUT_PC1 filename to store pct. change (to tp1) in <template>/stats/<OUT_PC1> (default: long.<stats>.<meas>-pc1.dat) --out-spc=OUT_SPC filename to store sym. pct. change in <template>/stats/<OUT_SPC> (default: long.<stats>.<meas>-spc.dat) --out-resid=OUT_RESID filename to store residual in <template>/stats/<OUT_RESID> (default: long.<stats>.<meas>-resid<resid>.dat), requires --resid <int> --out-stack=OUT_STACK filename to store stacked measure file <template>/stats/<OUT_STACK> (default: long.<stats>.<meas>-stack.dat) Stacked Tables: To output tables with results from all subjects --stack-avg=STACK_AVG full filename to stack temporal average tables (default no stacking) --stack-rate=STACK_RATE full filename to stack rate tables (default no stacking) --stack-pc1fit=STACK_PC1FIT full filename to stack pct. change to tp1fit tables (default no stacking) --stack-pc1=STACK_PC1 full filename to stack pct. change to tp1 tables (default no stacking) --stack-spc=STACK_SPC full filename to stack sym. pct. tables (default no stacking) --stack-resid=STACK_RESID full filename to stack residual tables (default no stacking)? Am I writing the code wrong?? I never got any long.<stats>.<meas>-pc1.dat file in <template>/stats/ folder except bunch of mgh files in <template>/surf/ folder. Thanks, Anwar -- Anwar S. Shatil Research Assistant Department of Medical Imaging Sunnybrook Health Sciences Centre Room AB204, 2075 Bayview Avenue Toronto, ON M4N 3M5 Tel: 416.480.6100 ext. 89617 Email: anwar.shatil(a)sunnybrook.ca This e-mail is intended only for the named recipient(s) and may contain confidential, personal and/or health information (information which may be subject to legal restrictions on use, retention and/or disclosure). No waiver of confidence is intended by virtue of communication via the internet. Any review or distribution by anyone other than the person(s) for whom it was originally intended is strictly prohibited. If you have received this e-mail in error, please contact the sender and destroy all copies.

2 4

Is voxel size resampled during recon-all? And different voxel size in longitudinal studies
by Daniel Ferreira 05 Sep '18

05 Sep '18

External Email - Use Caution Dear colleagues, I was wondering if resampling voxel size is done during recon-all. Also, I have data with voxel resolution of 1x1x1 mm at baseline and 1,2x1,2x1,2 at follow-up. I was wondering if recon-all does any computation by default (or can be performed by any way) that minimizes these differences in somehow. Thank you very much Dani -- *Daniel Ferreira, PhD, Assistant Professor* Division of Clinical Geriatrics; Department of Neurobiology, Care Sciences and Society Karolinska Institutet (Sweden) *Address: **Blickagången 16, 141 52 Huddinge | phone: +46 720128047 | email: daniel.ferreira.padilla(a)ki.se <daniel.ferreira.padilla(a)ki.se>*

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Re: [Freesurfer] fsaverage for a Left vs Right hemisphere Longitudinal
by Wang, Xiaoyu 04 Sep '18

04 Sep '18

External Email - Use Caution Thanks Martin, Yes, I did mean to have the right hemisphere added to the left hemisphere as a new time point. Can you explain on what you mean by run every subject only once? Do you mean to run xhemi for all of the subjects and then run a paired analysis? Xiaoyu

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Neuroimaging Research Engineer Position
by Florence M 31 Aug '18

31 Aug '18

External Email - Use Caution Title : Neuroimaging Research Engineer No. of Position(s) : One (1) position Location : Paris, France Starting date : November 2018 JOB DESCRIPTION The successful applicant will work in the Group of Clinical Research on Alzheimer Precision Medicine (GRC-APM) at the site of Pitié-Salpêtrière Hospital of Sorbonne University under the supervision of Prof. Harald Hampel, holder of AXA Research Fund & Sorbonne University Chair « sur le dépistage de la maladie d’Alzheimer». The GRC-APM has as main objective the advancements in detecting, treating, and preventing Alzheimer’s disease (AD) by the implementation of a Precision Medicine (PM) strategy. The successful applicant will be tasked with coding in efficient ways analytical methods and build internal capabilities and gears for these methods. He/she would also be responsible for setting up and running statistical and neuroimaging analysis pipelines for scientific studies. It would be expected for the Biomedical Research Engineer to regularly monitor and assess data quality for on-going projects and provide feedback to collaborators. Duties include: To develop MRI pipelines and data analyses in particular DTI data and their integration with structural MRI and functional MRI To support researchers in the team during the scientific writing process To manage the internal database, which may include the development of new user interfaces. Desired qualifications: Experienced in processing structural MRI and DTI neuroimaging data Demonstrated high level capacity for scripting with different languages, such as Python, R, MATLAB Familiarity with system administration, project and neuroimaging data management Familiarity with neurological concepts and/or experience with Alzheimer’s disease is desirable Ability to integrate multimodal data, including neuroimaging data, biological markers and genetic data will be appreciated. Education & experience Master's degree Biomedical Research Engineer or related field. Two years of relevant experience is highly desirable though not necessary Knowledge, skills and abilities: Strong analytical and organizational skills. Ability to learn and utilize relational databases, data integration, and statistics. Strong written and oral English communication skills. Ability to understand scientific literature, experimental procedures and their limitations, and current needs of the research community, as applied in clinical neuroscience and neuroimaging research. Position length: The position is supported for 4 years. However, candidates will be appointed for 1 year, with an extension possible based on progress Salary: 2,183 € gross / month Please send a brief letter of motivation and your detailed CV as one pdf (<2MB) to patrizia.chiesa(a)icm-institute.org

1 0

hippocampus subfields with T2
by Alexopoulos, Dimitrios 31 Aug '18

31 Aug '18

External Email - Use Caution We have a cohort of 10yo subjects for which we have acquired a 0.85mm isotropic T1-mprage and a 1mm isotropic T2-space. Is it possible or even recommended to try and generate better hippocampal segmentation in fressurfer 6.0 using both the T1 and T2, or does the T2 need to be of equal or better resolution than the T1? 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.

2 1

mri_fill unsuccessful in macaque
by Tello, Lawrence (NIH/NEI) [F] 30 Aug '18

30 Aug '18

External Email - Use Caution Hello, I am trying to generate an inflated surface for a macaque brain, but mri_fill has stopped working for this subject. Below is my command line and output. I specify the corpus callosum and pons as well. Any suggestions? mri_fill -CV 101 100 66 -PV 115 140 77 ./mri/wm/wm.nii.gz ./mri/filled/filled.mgz using voxel position (101, 100, 66) as corpus callosum seed point using voxel position (115, 140, 77) as pons seed point reading input volume...done. searching for cutting planes...INFO: volume does not have linear_transform set nor lta is given by option.-xform. INFO: use identity matrix as the talairach transform. INFO: use src volume parameters for the talairach volume. voxel to talairach voxel transform 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; Calculated talairach cc position (-8.26, -12.19, 56.63) Using the seed to calculate the cutting plane find_cutting_plane:seed point not in structure! Searching neighborhood... Looking for area (min, max) = (350, 1400) area[0] = 1 (min = 350, max = 1400), aspect = 1.00 (min = 0.10, max = 0.75) need search nearby using seed (101, 100, 66), TAL = (-8.3, -12.2, 56.6) talairach voxel to voxel transform 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; talairach cc position changed to (-8.26, -12.19, 56.63) Using voxel pons seed point, calculated talairach pons position (5.74, -1.19, 16.63) find_cutting_plane:seed point not in structure! Searching neighborhood... Looking for area (min, max) = (350, 790) area[0] = 1 (min = 350, max = 790), aspect = 1.00 (min = 0.60, max = 1.20) need search nearby using seed (115, 140, 77), TAL = (5.7, -1.2, 16.6) talairach voxel to voxel transform 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; done. seed_search_size = 9, min_neighbors = 5 search rh wm seed point around talairach space:(9.74, -12.19, 56.63) SRC: (119.00, 100.00, 66.00) could not find rh seed point around (119, 100, 66)

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Vertex coordinates of pial surface: mris_convert, read_surf(), tksurfer
by M. Jordan 30 Aug '18

30 Aug '18

External Email - Use Caution Hello, considering the surface 'lh.pial' of the reconAll process: When I apply 'mris_convert' in order to convert to .vtk, there is a shift with respect to the .pial file when viewing in freeview. When using the --cras_correction option for converting, the shift is gone. Nevertheless, the displayed vertex RAS coordinates in Freeview are different. Can anyone explain that? Respectively, what is '--cras_correction'actually doing? Moreover, when using the function 'read_surf()' in MATLAB to read 'lh.pial' I obtain the vertex coords, but when I compare the vertex with index 1923 to the corresponding "Vertex RAS" in tksurfer, there is a slightly mismatch. Can someone explain this? (I considered that MATLAB starts at index 1 and tksurfer at index 0!) I read, that tksurfer is actually displaying the coordinates of the 'orig' file and not the coords of the file which is actually visible? is that true? So the main questions are: - What are the coordinates of the 'lh.pial' file? (surface RAS / tkrRAS, or something different?) - Why and how do these coordinates change when converting (mris_convert) or reading in MATLAB (read_surf)? - Is vertex with index 1000, the same after mris_convert (vtk) and read_surf()? - Why there is a mismatch between the coordinates of a certain vertex in tksurfer and after read_surf - Does label2label only work with tkrRAS coordinates? Thank you very much!!

2 1

MRIread error
by Song, Da-Yea 30 Aug '18

30 Aug '18

External Email - Use Caution Hi everyone, I'm trying to pre-process subjects through the pipeline but keep getting a handful of subjects that error out within seconds of running them. The error message I get is: MRISread(/subjects/002_1006/surf/rh.white):could not open file When I go into the subject's folder, I find the rh.white file in the stats folder. I've run about 100 subjects without an issue but for some reason there are a few subjects that will stop processing with the same error message. Any suggestions or comments would be greatly appreciated. Thanks! Dayea ---------------------------------------------------------------------- Disclaimer: The materials in this e-mail are private and may contain Protected Information. Please note that e-mail communication is not encrypted by default. You have the right to request further emails be encrypted by notifying the sender. Your continued use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail.

2 5

Segmentation of hippocampal subfields and nuclei of the amygdala
by Meena M. Makary 30 Aug '18

30 Aug '18

External Email - Use Caution Hi; My Linux machine has FreeSurfer 6.0 with MATLAB runtime2012bLinux (MCRv80) which allows me to do the hippocampal subfields segmentation without errors. Now, I'd like to use [segmentHA_T1.sh] for hippocampal and nuclei of the amygdala segmentation which exists in the development version of 2018 but not in vr 6.0. I copied this bash file and other related files from the development version to my vr 6.0 /freesurfer/bin directory but I stuck with errors related to the MATLAB runtime version (it needs MCRv84). I downloaded runtime2014bLinux (MCRv84), but still same errors. Any recommendation to overcome this problem?. Will it be okay if I just replaced my vr6.0 /freesurfer/bin folder by the one from the recent development version? - given that I analyzed my data using recon-all by vr6.0. Thanks; --Meena -- *Meena M. Makary, Ph.D.* Assistant Professor | Cairo University <http://bmes.cufe.edu.eg/> Postdoctoral Fellow | Yale University School of Medicine <http://people.yale.edu/search/meena_beshara.profile> Postdoctoral Associate | The John B. Pierce Laboratory <http://jbpierce.org/postdoctoral-associates/> Treasurer | OHBM Student and Postdoc SIG <https://www.humanbrainmapping.org/i4a/pages/index.cfm?pageid=3449> 290 Congress Avenue, New Haven, CT 06519 +1 (475) 731-5592 <+1%20475-731-5592>

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Fwd: Biomedical Research Engineer Position
by Florence M 30 Aug '18

30 Aug '18

External Email - Use Caution Title : *Biomedical **Research Engineer* No. of Position(s) : One (1) position Location : Paris, France Starting date : November 2018 *JOB DESCRIPTION* The successful applicant will work in the Group of Clinical Research on Alzheimer Precision Medicine (GRC-APM) at the site of Pitié-Salpêtrière Hospital of Sorbonne University under the supervision of Prof. Harald Hampel, holder of AXA Research Fund & Sorbonne University Chair « sur le dépistage de la maladie d’Alzheimer». The GRC-APM has as main objective the advancements in detecting, treating, and preventing Alzheimer’s disease (AD) by the implementation of a Precision Medicine (PM) strategy. The successful applicant will be tasked with coding in efficient ways analytical methods and build internal capabilities and gears for these methods. He/she would also be responsible for setting up and running statistical and neuroimaging analysis pipelines for scientific studies. It would be expected for the Biomedical Research Engineer to regularly monitor and assess data quality for on-going projects and provide feedback to collaborators. *Duties include:* - To develop MRI pipelines and data analyses in particular DTI data and their integration with structural MRI and functional MRI - To support researchers in the team during the scientific writing process - To manage the internal database, which may include the development of new user interfaces. *Desired qualifications:* - Experienced in processing structural MRI and DTI neuroimaging data - Demonstrated high level capacity for scripting with different languages, such as Python, R, MATLAB - Familiarity with system administration, project and neuroimaging data management - Familiarity with neurological concepts and/or experience with Alzheimer’s disease is desirable - Ability to integrate multimodal data, including neuroimaging data, biological markers and genetic data will be appreciated. *Education & experience * Master's degree Biomedical Research Engineer or related field. Two years of relevant experience is highly desirable though not necessary *Knowledge, skills and abilities:* - Strong analytical and organizational skills. - Ability to learn and utilize relational databases, data integration, and statistics. - Strong written and oral English communication skills. - Ability to understand scientific literature, experimental procedures and their limitations, and current needs of the research community, as applied in clinical neuroscience and neuroimaging research. Position length: The position is supported for 4 years. However, candidates will be appointed for 1 year, with an extension possible based on progress Salary: 2,183 € gross / month Please send a brief letter of motivation and your detailed CV as one pdf (<2MB) to patrizia.chiesa(a)icm-institute.org

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Freesurfer August 2018