Freesurfer

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30134 discussions

Problem running recon-all in newly installed Ubuntu 16.04LTS
by Nasos Petridis 08 Dec '16

08 Dec '16

Hello freesurfer experts, I've recently set up a PC running Ubuntu 16.04LTS and tried to run a freesurfer version which was running well on another PC (also running Ubuntu 16.04LTS)...the nightly build for centos6 of 2016-09-03. I'm running the recon-all script. While running mri_ca_register, I get >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> label assignment complete, 7 changed (0.00%) det(m_affine) = 1.19 (predicted orig area = 6.7) label assignment complete, 8 changed (0.00%) Segmentation fault (core dumped) ERROR: mri_ca_register with non-zero status 139 but continuing despite the error >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> and a little bit later the program exits. Comparing the recon-all.log files from the runs in the two PCs, they appear identical until the above error appears, with the exception of the "main basin size", where the problematic PC gives a value which is 3.5% of that in the "good" PC. Any idea what may be going wrong with the new PC? Many thanks, Nasos

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mri_convert dcm 'Mosaic' 2 mgz
by Marianna Riello 07 Dec '16

07 Dec '16

Dear all, I am wondering whether mri_convert can compute .mgz files for the reconstructions with the 'Mosaic Format SIEMENS DICOM files'. I have been computing .mgz with the enhanced format .dcm so far, and it always worked. I have used mri_convert to compute .mgz from .nii (I previously transformed the mosaic .dcm format in nifti with mricron but the reconstruction failed) Thanks in advance, Marianna

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Optseq: psdwinMAX value for events of 8s?
by Xavier Guell Paradis 07 Dec '16

07 Dec '16

Dear FS team, I have one short question regarding Optseq: What is the recommended psdwinMAX value for events of 8s? I have read in this forum that events of 3s should have a psdwinMAX of 21s or even 24s; does this mean that events of 8s should have a psdwinMAX of 26-29s? Thank you very much, Xavier. Xavier Guell Paradis, M.D. Visiting Scientist Massachusetts Institute of Technology McGovern Institute for Brain Research Office: 46-4033A Phone: (617) 324-4355 Email: xaviergp(a)mit.edu

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Treating multiple subjects as a single subject in TRACULA
by Vivek Subramanian 07 Dec '16

07 Dec '16

Hi, I have DWI data from two subjects acquired using b-values of 0 for the B0's and 700 for the DWI's. There are 10 B0's and 60 DWI's in each dataset. I was successfully able to follow the instructions to use TRACULA on data from a single subject (recon-all; then trac-all -prep, -bedp, and -path), but I now want to infer a "group tractography" by running TRACULA on data from both subjects in the group as if they were from the same subject. This should yield one tractography for the entire group. I have registered all T1's to a common MNI template so they have the same dimensions. Cortical reconstruction was performed on the average of the subjects' T1s. When I run TRACULA, however, rather than pulling the bvecs from the DWI's, it takes them from a file called gradient_mgh_dti60.gdt, which is located under the Freesurfer installation. This file only contains 60 diffusion gradient directions. These closely match those of the 60 DWI files from one subject (but are not exactly the same), but because the contents of gradient_mgh_dti60.gdt are only being copied over once to the bvecs file in the subject directory, the bvecs file has only 60 sets of entries (+10 sets of 0's for the set of B0's). In other words, the file contains three rows of data (one for each spatial dimension), each with 10 zeros followed by 60 bvec entries. I expect there to be three rows of data, with 10 0's, followed by 60 bvec entries, followed by 10 0's, followed by 60 bvec entries. The bvals file, however, is fine; i.e. there are 10 0's, followed by 60 700's, followed by 100 0's, followed by 60 700's. This causes the -prep phase of trac-all to exit with errors when dtifit fails because the bvals and bvecs files don't have the same number of entries. I'm wondering what I need to do to get around this issue so the data can all be treated as if it came from the same subject and the bvecs are taken from the DWI's rather than from the gradient_mgh_dti60.gdt file. If you'd like, I can upload the bvecs and bvals files that trac-all -prep generates and also the output stream to the terminal. Thank you, Vivek

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Re: [Freesurfer] 4 questions regarding Optseq (FS mailing list)
by Douglas N Greve 07 Dec '16

07 Dec '16

Hi Xavier, please remember to post to the FS list. Answers below On 12/07/2016 08:19 AM, Xavier Guell Paradis wrote: > Dear Dr. Greve, > Thank you very much for your reply. I have one last question, which I > think is a very basic concept that I understood wrong: > If I want to compare finger tapping (for periods of 8s) vs. rest (for > periods of 8s), shouldn't I enter "fingertapping" and "rest" as two > conditions (i.e. two events, "ev") in Optseq? No, you do not. > If I do this, then Optseq will generate inter-stimulus intervals, and > my schedule will look more or less like this: > > Fingertapping 8s > NULL 1s > Rest 8s > NULL 4s > Rest 8s > NULL 2s > Fingertapping 8s > etc... > > My question #3 made reference to this: does it make sense that "NULL" > (the interstimulus interval) and "Rest" are essentially the same thing > (the subject is viewing a fixation cross and not doing finger > tapping)? Or should I use only one condition (Fingertapping) (i.e. > only one "event", "ev"), and compare BOLD signal in the fingertapping > condition with BOLD signal in the NULL condition? I would use one condition. > I think the basic question that I am not understanding correctly is > this: If one of the conditions that we want to compare is simply > viewing a fixation cross, should we include this as a condition in > Optseq (i.e. as an event, "ev"; which is the "Rest" in the example > schedule above) or should we just use the inter-stimulus interval > (NULL) as our "viewing a fixation cross" condition? I would not include Rest as a condition in optseq > > Thank you very much, > Xavier Guell. > > Xavier Guell Paradis, M.D. > Visiting Scientist > Massachusetts Institute of Technology > McGovern Institute for Brain Research > Office: 46-4033A > Phone: (617) 324-4355 > Email: xaviergp(a)mit.edu > > On 12/06/2016 04:57 PM, Xavier Guell Paradis wrote: > > > > Dear FS team, > > > > We are designing an fMRI experiment that has to include one motor, one > > cognitive and one affective task. We would like to use a rapid > > event-related design because we want to do MVPA to classify patients > > vs controls. We have 4 questions regarding Optseq: > > > > 1) We are designing a task where subjects either rest (while viewing a > > fixation cross) or tap their right index finger (while viewing a > > fixation cross surrounded by a green circle). Does it make sense, for > > a rapid-event related design, to make subjects tap their right index > > finger for 8 seconds or rest for 8 seconds, or should we decrease the > > number of seconds? > > > From an analysis standpoint, that is fine. optseq will set the number > of seconds for the rest period (you can set the bounds with --tnullmin > and --tnullmax) > > > > 2) We have a similar question for a task where subjects view images > > which are either happy, scary or neutral. Each image lasts 1.5s. We > > would like to group images in groups of 4 so that the emotional > > response is more intense (if we are interested in making the subject > > feel happiness we would prefer that subjects see 4 consecutive happy > > images, rather than one happy image and then one scary image and then > > one happy image). Therefore, we have groups of 4 images and each group > > lasts 6s (4x1.5s). Does it make sense, for a rapid-event related > > design, to consider that each stimulus lasts 6 seconds (this includes > > 4 images of 1.5s of the same emotional category); or should we > > decrease the number of seconds; or simply present each image of 1.5s > > individually? > > > Again, ok. > > > > 3) We are designing a task where subjects either rest (while viewing a > > fixation cross) or tap their right index finger (while viewing a > > fixation cross surrounded by a green circle). Optseq generates > > jittered inter-stimulus intervals, and during inter-stimulus intervals > > subjects will view a fixation cross and rest. Does it make sense that > > subjects are seeing the same thing in the ?rest? condition and in the > > inter-stimulus intervals? (in both cases, a fixation cross is shown in > > the screen and subjects are resting) > > > Isn't this the same as #1? I guess I don't understand how you plan to > analyze your data. Is some of the rest different than other parts of the > rest? > > > > 4) We are designing a go/nogo task where subjects have to press a > > button only when a stimulus of a particular shape (square or circle) > > and color (yellow or purple) is presented. Each stimulus is presented > > for 2s. We would like to change the instructions every 12 stimuli, and > > we would like to change the instructions 3 times. To change the > > instructions, we would have to show text to the subjects for 15 > > seconds explaining the new instructions (e.g. ?press the button when > > you see a purple square?). Is there any way to include the > > instructions in Optseq; or should we run Optseq for 12 stimuli, keep > > the best 4 schedules, and then include a 30 seconds pause between each > > schedule of 12 stimuli to allow the hemodynamic response to return to > > baseline while presenting the new instructions? > > > There is not a way to include the instructions in optseq. I would keep > the best 12-stimulus sequences from optseq. You don't need to wait 30 > sec, 15 sec should be ok > > > > Thank you very much, > > > > Xavier Guell. > > > > > > > > Xavier Guell Paradis, M.D. > > Visiting Scientist > > Massachusetts Institute of Technology > > McGovern Institute for Brain Research > > Office: 46-4033A > > Phone: (617) 324-4355 > > Email: xaviergp(a)mit.edu > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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Volumetric Group Analysis: asegstats2tbale result to plot a z-score map for the segmentation
by Hao wen 07 Dec '16

07 Dec '16

Hello, FS experts: I have a question for visualizing statistical analysis asegstats2tbale result into a map like what we have done in qdec, which uses the thickness information, so if i want to use the volume information of the different segmentation volume, and after doing z-score for two groups, how can I visualize it into a z map??? For example, for the volumetric group analysis, I compute the z-scores for the different subcortical volumes between these two group, how do i visualize the result in sphere??? Really need your help Any help will be appreciated Hao

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'Did not find any volume geometry information in the surface'
by Shady Rahayel 06 Dec '16

06 Dec '16

Hi, I was conducting GLM analysis using the command line. Everything seemed to work fine until I wanted to visualize the uncorrected significance map using the following command (my glmdir folder for the contrast is lh.scheme1.glmdir): freeview -f $SUBJECTS_DIR/fsaverage/surf/lh.inflated:annot=aparc.annot:overlay=$SUBJECTS_DIR/qdec/lh.scheme1.glmdir/scheme1/sig.mgh:overlay_threshold=4,5 -viewport 3d 'Did not find any volume geometry information in the surface' appears in the terminal window. In freeview, only the fsaverage lh.inflated file appears. I am wondering whether it is actually related to my experimental scheme. I want to study the relationship between cortical volume and variable X, while isolating for the effects of 4 factors (2 discrete A and B, 2 continuous C and D). So I've created an FSGD file: GroupDescriptorFile 1 Title xxx Class A1B1 Class A1B2 Class A2B1 Class A2B2 Variables X C D Input .... And I have created a scheme1.mtx contrast matrix that goes like this: 0 0 0 0 0.25 0.25 0.25 0.25 0 0 0 0 0 0 0 0 So that only the slope for X is modelled while isolating for the effect of everything else. I am however unsure of whether it is the proper way to conceptualize the issue. I've done mris_preproc --fsgd scheme1.fsgd --cache-in volume.fwhm15.fsaverage --target fsaverage --hemi lh --out lh.scheme1.volume.15.mgh And then mri_glmfit --y lh.scheme1.volume.15.mgh --fsgd scheme1.fsgd dods --C scheme1.mtx --surf fsaverage lh --cortex --glmdir lh.scheme1.glmdir I am clueless of where may be my mistake. Thank you Shady -- *Shady Rahayel* Étudiant au Ph.D. en neuropsychologie R/I Université du Québec à Montréal Centre d'Études Avancées en Médecine du Sommeil Hôpital du Sacré-Coeur de Montréal

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4 questions regarding Optseq
by Xavier Guell Paradis 06 Dec '16

06 Dec '16

Dear FS team, We are designing an fMRI experiment that has to include one motor, one cognitive and one affective task. We would like to use a rapid event-related design because we want to do MVPA to classify patients vs controls. We have 4 questions regarding Optseq: 1) We are designing a task where subjects either rest (while viewing a fixation cross) or tap their right index finger (while viewing a fixation cross surrounded by a green circle). Does it make sense, for a rapid-event related design, to make subjects tap their right index finger for 8 seconds or rest for 8 seconds, or should we decrease the number of seconds? 2) We have a similar question for a task where subjects view images which are either happy, scary or neutral. Each image lasts 1.5s. We would like to group images in groups of 4 so that the emotional response is more intense (if we are interested in making the subject feel happiness we would prefer that subjects see 4 consecutive happy images, rather than one happy image and then one scary image and then one happy image). Therefore, we have groups of 4 images and each group lasts 6s (4x1.5s). Does it make sense, for a rapid-event related design, to consider that each stimulus lasts 6 seconds (this includes 4 images of 1.5s of the same emotional category); or should we decrease the number of seconds; or simply present each image of 1.5s individually? 3) We are designing a task where subjects either rest (while viewing a fixation cross) or tap their right index finger (while viewing a fixation cross surrounded by a green circle). Optseq generates jittered inter-stimulus intervals, and during inter-stimulus intervals subjects will view a fixation cross and rest. Does it make sense that subjects are seeing the same thing in the “rest” condition and in the inter-stimulus intervals? (in both cases, a fixation cross is shown in the screen and subjects are resting) 4) We are designing a go/nogo task where subjects have to press a button only when a stimulus of a particular shape (square or circle) and color (yellow or purple) is presented. Each stimulus is presented for 2s. We would like to change the instructions every 12 stimuli, and we would like to change the instructions 3 times. To change the instructions, we would have to show text to the subjects for 15 seconds explaining the new instructions (e.g. “press the button when you see a purple square”). Is there any way to include the instructions in Optseq; or should we run Optseq for 12 stimuli, keep the best 4 schedules, and then include a 30 seconds pause between each schedule of 12 stimuli to allow the hemodynamic response to return to baseline while presenting the new instructions? Thank you very much, Xavier Guell. Xavier Guell Paradis, M.D. Visiting Scientist Massachusetts Institute of Technology McGovern Institute for Brain Research Office: 46-4033A Phone: (617) 324-4355 Email: xaviergp(a)mit.edu

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Problem with mri_vol2surf
by Ilaria Mazzonetto 06 Dec '16

06 Dec '16

Hi Freesurfer User, I would like to map a volume to a surface. I have a T1 image (SubjX) with resolution 1x1x1 and a gray matter mask with resolution 6x6x6. The voxels in the lower resolution image (gm_values.nii) have zero value if they are not in the gray matter and a value between 0.1 and 20 if they are in the gray matter. What I want to do is mapping this values in the pial surface. I runned recon-all with T1 image and I coregistered the lower resolution image (the mask) to higher resolution image with FSL (gm_values2anat.nii). Then I runned mri_vol2surf -- src gm_values2anat.nii --regheader SubjX --hemi lh --surf pial --o gm_values_lhsurf.mgh. I do not understand what the options for surface normal projection mean. I inspected the result with tksurfer, setting fminmask 0 20, and there are a lot of holes. Do you think there is something wrong in what I did? Any help would be greatly appreciated. Regards. Ilaria

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aparcstat2label command result does not include corpuscallosum label
by Hao wen 06 Dec '16

06 Dec '16

Hello, freesurfer experts: I have a question, recently, I use the aparcstats2label comamnd, and get the result file, and I use tksurfer to display the desikan atlas(?h.aparc.annot), and I want to corresponds the labels between this two, but in my aparcstats2label result file, i can not find the corpuscallosum which is the No.4 label in tksurfer, to be specific, here is the label ID in desikan atlas in tksurfer: aparc_lables = ['unknown', 'bankssts', 'caudalanteriorcingulate', 'caudalmiddlefrontal', 'corpuscallosum', 'cuneus', 'entorhinal', 'fusiform', 'inferiorparietal', 'inferiortemporal', 'isthmuscingulate', 'lateraloccipital', 'lateralorbitofrontal', 'lingual', 'medialorbitofrontal', 'middletemporal', 'parahippocampal', 'paracentral', 'parsopercularis', 'parsorbitalis', 'parstriangularis', 'pericalcarine', 'postcentral', 'posteriorcingulate', 'precentral', 'precuneus', 'rostralanteriorcingulate', 'rostralmiddlefrontal', 'superiorfrontal', 'superiorparietal', 'superiortemporal', 'supramarginal', 'frontalpole', 'temporalpole', 'transversetemporal', 'insula'] which has 36 labels, and I dont understand which label is unknow.... on the contrary, the result from aparcstat2table have 36 columns(includint subject_id and meanthickness), so bacially, they have just 34 labels add one 'unknown', it should have 35 labels, but I did not find the lable 'corpuscallosum', Can someone help me??? The result file for aparcstat2table file is attached:) Thanks in advance

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