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30080 discussions

mri_vol2surf with --projopt
by Kamiya Kouhei 13 Jun '22

13 Jun '22

External Email - Use Caution Dear FreeSurfer experts, I have a question on the usage of mri_vol2surf's option, "--projopt". What I want to do is to map the diffusion scalar value (like mean diffusivity [MD]) to the cortical surface. Though mri_vol2surf with --projfrac 0.5 worked pretty well, I also tried with --projopt which I assumed to yield better dealing with the partial volume effects. However, when I run with --projopt, I encountered the following errors. ....... error: GM estimation at vno 31257 couldn't find enough samples error: GM estimation at vno 31258 couldn't find enough samples ....... It looks the code tells me there is not enough data to solve the problem. Could you please instruct me what should I do to use mri_vol2surf with --projopt ? My diffusion maps are in 1.7mm isotropic voxel and aligned with anatomical T1w with BBregister, and I used the code as below. ################ tkregister2 --mov ${SUBJECTS_DIR}/${subject}/mri/norm.mgz --s ${subject} --regheader --reg regheader.subject.dat --noedit mri_compute_volume_fractions regheader.subject.dat ${SUBJECTS_DIR}/${subject}/mri/norm.mgz pvf # this gave me pvf.wm.mgz, pvf.csf.mgz, pvf.cortex.mgz, which are in 1mm voxel mv pvf.cortex.mgz pvf.gm.mgz # rename to pvf.gm.mgz to be compatible with the file name that appears in mri_vol2surf code mri_vol2surf --mov MD.nii.gz --regheader ${subject} --hemi lh --surf white --projopt pvf --o lh.MD_pvf.GM.mgz ################ Respectfully yours, Kouhei Kamiya

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Monte Carlo for lme
by Knut J Bjuland 11 Jun '22

11 Jun '22

External Email - Use Caution Dear Freesurfer experts, I am looking into Monte Carlo simulation to control for multiple comparisons for lme in Matlab. Are there any good library that has implemented this in Matlab? Best regards Knut Jørgen Bjuland PhD

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traculina errors in -prep process
by Emmanuel Rodríguez Silva 11 Jun '22

11 Jun '22

External Email - Use Caution Hello, I'm Emmanuel from Mexico. I'm currently working with the pipeline of traculina, but during the first process (-prep) I found an error that says: "can't open orig/COR-.inf" and below that message there appears also: "ERROR: tkregister2_cmdl". I figured out that infant freesurfer does not generate such a directory, as freesurfer does. I know that inside the 'orig' directory freesurfer locates a file called t1.mgz, or something like that. Do you know how I can solve this issue? I have already tried to create manually these files, but it did not work ------------------------------------------------------------------------------- I'm using the latest version of freesurfer, My O.S. is ubuntu 20.04 I'll appreciate your help, best regards -- Saludos cordiales Emmanuel Rodríguez Silva Contacto: (044) 55 59 97 76 18 Licenciado en Manejo Sustentable de Zonas Costeras *UNAM*

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Postdoctoral Research Fellow position in Neuroimaging
by Aganj, Iman 10 Jun '22

10 Jun '22

Good afternoon, The Laboratories for Computational Neuroimaging<https://www.nmr.mgh.harvard.edu/lab/lcn> at the Athinoula A. Martinos Center for Biomedical Imaging invites applications for a Postdoctoral Research Fellow position at the Massachusetts General Hospital and Harvard Medical School. The project will consist of diffusion-MRI harmonization and brain connectivity analysis, with application in studying Parkinson's disease. The appointment is for two years with the possibility of a third year based on performance and the availability of funding. The project involves reducing inter-site variability of (a.k.a. harmonizing) diffusion-MRI datasets from multiple centers, analyzing human brain networks, and examining the relationship of brain connections with stages of Parkinson's disease. The Research Fellow will be supervised by Dr. Iman Aganj, in close collaboration with Dr. Bruce Fischl. The candidate is required to have: * a Ph.D. in engineering, neuroscience, or a related field by the start date, * strong programming skills in MATLAB, Python, or a similar environment, and * experience with diffusion MRI analysis and/or MRI data harmonization. Familiarity and experience with any of the following will be a plus: * connectomics, machine/deep learning, graph theory, neurodegenerative (esp. Parkinson's disease) studies, mathematical modeling. Interested applicants are invited to send a cover letter describing research interests and experience, an up-to-date CV, and names and contact information of three references to: iaganj(a)mgh.harvard.edu<mailto:iaganj@mgh.harvard.edu> Best regards, Iman Aganj Assistant Professor of Radiology Harvard Medical School Associate Investigator Athinoula A. Martinos Center for Biomedical Imaging Massachusetts General Hospital

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Extracting average T1w/T2w values from surface
by Austin Boroshok 09 Jun '22

09 Jun '22

Hello, I have created surfaces that contain T1w/T2w ratios (see Glasser & van Essen, 2011; Ganzetti et al., 2014 for details). I am looking to extract the average T1w/T2w value for each of the 7 Yeo networks from the surfaces. We wish to extract intensities from the surface to avoid partial voluming effects that we have observed when extracting whole-brain T1w/T2w values from the T1w/T2w ratio maps (volumes) using a cortical gray matter mask. I have previously tried using mri_anatomical_stats and mri_segstats to do this without success. I received the following errors with each command, respectively: mri_anatomical_stats: command: mris_anatomical_stats -t lh_<T1w/T2w_ratio_surface>.mgh -a <freesurfer_path>/lh.Yeo2011_7Networks_N1000.annot -b subject lh output + error: using thickness file lh_<T1w/T2w_ratio_surface>.mgh. computing statistics for each annotation in <freesurfer_path>/lh.Yeo2011_7Networks_N1000.annot. reading volume /subject/mri/wm.mgz... reading input surface /subject/surf/lh.white... Using TH3 vertex volume calc Total face volume 306338 Total vertex volume 302976 (mask=0) reading input pial surface /subject//urf/lh.pial... reading input white surface /subject/surf/lh.white... ERROR: number of vertices in lh_<T1w/T2w_ratio_surface>.mgh does not match surface (163842,154532) (And the table column of “average cortical thickness” (in my case, T1w/T2w ratio) are all 0.000s for the 7 Yeo Networks) mri_segstats: Command: mri_segstats --i lh_MM_cbpd_brannon_age_gender_n157_glm_fwhm_src5trg5.mgh --seg ../../../../../freesurfer/fsaverage/label/lh.Yeo2011_7Networks_N1000.annot --avgwf test.dat output + error: Loading ../../../../../freesurfer/fsaverage/label/lh.Yeo2011_7Networks_N1000.annot mri_read(): couldn't determine type of file ../../../../../freesurfer/fsaverage/label/lh.Yeo2011_7Networks_N1000.annot ERROR: loading ../../../../../freesurfer/fsaverage/label/lh.Yeo2011_7Networks_N1000.annot I am running macOS Monterery 12.4, Freesurfer 6.0.0. Can anyone please advise if I am using mri_anatomical_stats or mri_segstats incorrectly, or if there is a better way to extract average T1w/T2w values from the surface directly? Thank you in advance for any help. Best, Austin External Email - Use Caution

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vertex out of range mris_label2annot
by Benjamin Deck 09 Jun '22

09 Jun '22

External Email - Use Caution Hi freesurfer experts, I am attempting to create a custom annotation file with the following LUT and call: mris_label2annot --s sub-DAEK --hemi lh \ --ctab sub-DAEK_yeoLUT.txt \ --a yeo2011nodes \ --maxstatwinner \ --l Net_10_ROIs_1_lh_native_dil2.label \ --l Net_10_ROIs_1_rh_native_dil2.label \ --l Net_11_ROIs_1_lh_native_dil2.label \ --l Net_11_ROIs_1_rh_native_dil2.label \ --l Net_12_ROIs_1_lh_native_dil2.label \ --l Net_12_ROIs_1_rh_native_dil2.label \ --l Net_12_ROIs_2_lh_native_dil2.label \ .....many other labels LUT: 0 Unknown 0 0 0 0 1 Net_10_ROIs_1_lh_native 5 5 5 0 2 Net_10_ROIs_1_rh_native 25 5 25 0 3 Net_11_ROIs_1_lh_native 25 100 40 0 4 Net_11_ROIs_1_rh_native 70 130 180 0 5 Net_12_ROIs_1_lh_native 100 100 0 0 6 Net_12_ROIs_1_rh_native 196 58 250 0 .....many others However, when I run the above command it breaks with the following issue: Reading ctab sub-DAEK_yeoLUT.txt Number of ctab entries 104 7.2.0 cwd /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels cmdline mris_label2annot --s sub-DAEK --hemi lh --ctab sub-DAEK_yeoLUT.txt --a yeo2011nodes --maxstatwinner --l Net_10_ROIs_1_lh_native_dil2.label --l Net_10_ROIs_1_rh_native_dil2.label --l Net_11_ROIs_1_lh_native_dil2.label --l Net_11_ROIs_1_rh_native_dil2.label --l Net_12_ROIs_1_lh_native_dil2.label --l Net_12_ROIs_1_rh_native_dil2.label --l Net_12_ROIs_2_lh_native_dil2.label --l Net_12_ROIs_2_rh_native_dil2.label --l Net_13_ROIs_1_lh_native_dil2.label --l Net_13_ROIs_1_rh_native_dil2.label --l Net_13_ROIs_2_lh_native_dil2.label --l Net_13_ROIs_2_rh_native_dil2.label --l Net_13_ROIs_3_lh_native_dil2.label --l Net_13_ROIs_3_rh_native_dil2.label --l Net_13_ROIs_4_lh_native_dil2.label --l Net_13_ROIs_4_rh_native_dil2.label --l Net_13_ROIs_5_lh_native_dil2.label --l Net_14_ROIs_1_lh_native_dil2.label --l Net_14_ROIs_1_rh_native_dil2.label --l Net_14_ROIs_2_lh_native_dil2.label --l Net_14_ROIs_2_rh_native_dil2.label --l Net_14_ROIs_3_lh_native_dil2.label --l Net_14_ROIs_3_rh_native_dil2.label --l Net_14_ROIs_4_lh_native_dil2.label --l Net_14_ROIs_4_rh_native_dil2.label --l Net_14_ROIs_5_lh_native_dil2.label --l Net_14_ROIs_5_rh_native_dil2.label --l Net_15_ROIs_1_lh_native_dil2.label --l Net_15_ROIs_1_rh_native_dil2.label --l Net_16_ROIs_1_lh_native_dil2.label --l Net_16_ROIs_1_rh_native_dil2.label --l Net_16_ROIs_2_lh_native_dil2.label --l Net_16_ROIs_2_rh_native_dil2.label --l Net_16_ROIs_3_rh_native_dil2.label --l Net_17_ROIs_1_lh_native_dil2.label --l Net_17_ROIs_1_rh_native_dil2.label --l Net_17_ROIs_2_lh_native_dil2.label --l Net_17_ROIs_2_rh_native_dil2.label --l Net_17_ROIs_3_lh_native_dil2.label --l Net_17_ROIs_3_rh_native_dil2.label --l Net_17_ROIs_4_lh_native_dil2.label --l Net_17_ROIs_4_rh_native_dil2.label --l Net_18_ROIs_1_lh_native_dil2.label --l Net_18_ROIs_1_rh_native_dil2.label --l Net_18_ROIs_2_lh_native_dil2.label --l Net_18_ROIs_2_rh_native_dil2.label --l Net_18_ROIs_3_lh_native_dil2.label --l Net_18_ROIs_3_rh_native_dil2.label --l Net_18_ROIs_4_lh_native_dil2.label --l Net_18_ROIs_4_rh_native_dil2.label --l Net_18_ROIs_5_lh_native_dil2.label --l Net_19_ROIs_1_lh_native_dil2.label --l Net_19_ROIs_1_rh_native_dil2.label --l Net_2_ROIs_1_lh_native_dil2.label --l Net_2_ROIs_1_rh_native_dil2.label --l Net_2_ROIs_2_lh_native_dil2.label --l Net_2_ROIs_2_rh_native_dil2.label --l Net_3_ROIs_1_lh_native_dil2.label --l Net_3_ROIs_1_rh_native_dil2.label --l Net_3_ROIs_2_lh_native_dil2.label --l Net_3_ROIs_2_rh_native_dil2.label --l Net_3_ROIs_3_lh_native_dil2.label --l Net_3_ROIs_3_rh_native_dil2.label --l Net_4_ROIs_1_lh_native_dil2.label --l Net_4_ROIs_1_rh_native_dil2.label --l Net_5_ROIs_1_lh_native_dil2.label --l Net_5_ROIs_1_rh_native_dil2.label --l Net_5_ROIs_2_lh_native_dil2.label --l Net_5_ROIs_2_rh_native_dil2.label --l Net_5_ROIs_3_lh_native_dil2.label --l Net_5_ROIs_3_rh_native_dil2.label --l Net_5_ROIs_4_lh_native_dil2.label --l Net_5_ROIs_4_rh_native_dil2.label --l Net_6_ROIs_1_lh_native_dil2.label --l Net_6_ROIs_1_rh_native_dil2.label --l Net_6_ROIs_2_lh_native_dil2.label --l Net_6_ROIs_2_rh_native_dil2.label --l Net_6_ROIs_3_lh_native_dil2.label --l Net_6_ROIs_3_rh_native_dil2.label --l Net_7_ROIs_1_lh_native_dil2.label --l Net_7_ROIs_1_rh_native_dil2.label --l Net_7_ROIs_2_lh_native_dil2.label --l Net_7_ROIs_2_rh_native_dil2.label --l Net_7_ROIs_3_rh_native_dil2.label --l Net_8_ROIs_1_lh_native_dil2.label --l Net_8_ROIs_1_rh_native_dil2.label --l Net_8_ROIs_2_lh_native_dil2.label --l Net_8_ROIs_2_rh_native_dil2.label --l Net_8_ROIs_3_lh_native_dil2.label --l Net_8_ROIs_3_rh_native_dil2.label --l Net_8_ROIs_4_lh_native_dil2.label --l Net_8_ROIs_4_rh_native_dil2.label --l Net_8_ROIs_5_lh_native_dil2.label --l Net_8_ROIs_5_rh_native_dil2.label --l Net_8_ROIs_6_rh_native_dil2.label --l Net_9_ROIs_1_lh_native_dil2.label --l Net_9_ROIs_1_rh_native_dil2.label --l Net_9_ROIs_2_lh_native_dil2.label --l Net_9_ROIs_2_rh_native_dil2.label --l Net_9_ROIs_3_lh_native_dil2.label --l Net_9_ROIs_3_rh_native_dil2.label --l Net_9_ROIs_4_rh_native_dil2.label --l Net_9_ROIs_5_rh_native_dil2.label --l Net_9_ROIs_6_rh_native_dil2.label sysname Linux hostname LAPTOP-LPS9CH5E machine x86_64 user bdeck8317 subject sub-DAEK hemi lh SUBJECTS_DIR /mnt/c/Users/Ben/freesurfer/subjects ColorTable sub-DAEK_yeoLUT.txt AnnotName yeo2011nodes nlables 104 LabelThresh 0 0.000000 Loading /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/surf/lh.orig 1 328965 Net_10_ROIs_1_lh_native 2 1639705 Net_10_ROIs_1_rh_native WARNING: vertex 210080 maps to multiple labels! (overwriting) WARNING: vertex 210124 maps to multiple labels! (overwriting) WARNING: vertex 210125 maps to multiple labels! (overwriting) WARNING: vertex 210151 maps to multiple labels! (overwriting) WARNING: vertex 210172 maps to multiple labels! (overwriting) WARNING: vertex 210173 maps to multiple labels! (overwriting) WARNING: vertex 211157 maps to multiple labels! (overwriting) WARNING: vertex 211158 maps to multiple labels! (overwriting) ERROR: Net_10_ROIs_1_rh_native_dil2.label, n=9538, vertex 254077 out of range Any thoughts on the fix for this issue? Thanks -- *Benjamin L. Deck* *Doctoral Student* *Applied Cognitive and Brain Sciences* *Department of Psychological and Brain Sciences* *Drexel University* <https://secure-web.cisco.com/1VCP2x7hEk3S0x-5t1wZJvcOAgVvGsjI-A6YfmqQ3APzc6…> Virus-free. http://secure-web.cisco.com/1uytf0Jop2l-hBvj0LkzK1ihVI480a63685NQS301iCX6X3… <https://secure-web.cisco.com/1YnAF7HOvTmiAw4b2v-qinSbPinE1DozllhrvyX8ipXNXh…> <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>

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using freeview7 to set manual paths
by Valeria Centanino 09 Jun '22

09 Jun '22

External Email - Use Caution Hello, I need to set manual paths on inflated surfaces, and I would like to use FreeView7, but I couldn't find any option to save the path after creating it. Could you please tell me if this is implemented in FreeView7 and, if yes, how can I do it? Thanks very much, Valeria

2 1

labels in anatomical space
by Sam W 09 Jun '22

09 Jun '22

External Email - Use Caution Hello! I have a label in freesurfer space, and I would like it to be in anatomical space. Is this possible? Best regards, Sam

3 6

HRF with derivatives: results
by Laura Doll 09 Jun '22

09 Jun '22

External Email - Use Caution Hi everyone, I need some help regarding the SPM-HRF with two derivatives: Where can I find the actual function that was used for the analysis? I am mostly interested in the peak latency, but would also appreciate if I can check the other parameters of the function somewhere. Best, Laura

2 8

creating. or replacing a label of choice in aseg atlas
by Ramtilak Gattu 09 Jun '22

09 Jun '22

External Email - Use Caution Hi, We are interested in replacing a couple of labels in aseg atlas with our own roi's already in the same space as of "aseg.mgz" atlas in the fsaverage folder. What would be the best way to do this? Could someone help or guide me if anyone has done something similar to this query? Can I just add the regions (in the form of 3d masks) to the aseg atlas and create aseg_modified.mgz and later replace the aseg.mgz with aseg_modified.gz and rename the aseg_modified.mgz back to aseg.mgz. If I follow this procedure and run "recon-all" will the aseg_stats will give me volumes based on the new volumes? -- Regards Tilak

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