Freesurfer

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19 participants
30088 discussions

recon-all and corrected hemispheres
by Ayaz, Muhammad 11 Aug '11

11 Aug '11

Dear All, I acquired the images using Phillips scanner. I converted the images from par into analyze using MRIcro. I noticed that images were flipped when I view them in the axial plane, i.e. when I look at the images on the computer screen the Right hemisphere (where we tapped the fish oil tablet) is on the right side of the image. Should I flip the images before running through the recon-all? Thanks Ayaz The information contained in this message and any attachments is intended only for the use of the individual or entity to which it is addressed, and may contain information that is PRIVILEGED, CONFIDENTIAL, and exempt from disclosure under applicable law. If you are not the intended recipient, you are prohibited from copying, distributing, or using the information. Please contact the sender immediately by return e-mail and delete the original message from your system.

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Re: [Freesurfer] long_mris_slopes error
by Martin Reuter 11 Aug '11

11 Aug '11

Hi Hyojeong, on the wiki release notes is a fixed mris_calc binary. Best, Martin On Aug 11, 2011, at 8:00 AM, Administrator wrote: > Dear Martin, > > I've received the same error as below which discussed previously. > Would you tell me if you managed build a fixed file, please? > > Hyojeong Lee > Hallym University College of Medicine, Anyang, Korea > > > long_mris_slopes --qdec ./qdec/long.qdec.tem_VNL01_KCY.dat --meas thickness --hemi lh --do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label --time weeks --qcache fsaverage > ...... > =============================================================================== > SUBJECT VN1 fwhm 0 computing SPC > > mris_calc -o /Volumes/data/freesurfer_analysis/VN_longitudinal/VN1/surf/lh.long.thickness-spc.fwhm0.mgh ./tmp-VN1_lh_thickness_OLudiD/beta1.mgh div ./tmp-VN1_lh_thickness_OLudiD/beta0.mgh > > ERROR -10 : mris_calc compute sym. pct. change (spc) problem? > > >

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Re: [Freesurfer] Volumetric analysis of thalamus in freesurfer
by Knut J Bjuland 11 Aug '11

11 Aug '11

Hi Bruce I am now responding to the list as well. I have a group with different subjects where I wish to correlate thalamus volume with gender difference. Though I have extract the data using asegstats2table. I wish to be sure that the group difference is correct. Due to this reason I wish to use multiple comparsion within Freesurfer for instant FDR. I have some trouble figuring out --iv volmeasfile or how to use an label to include thalamus but exclude everything else? Knut J Knut J On 08/11/2011 08:42 PM, Bruce Fischl wrote: > Hi Knut > > you should respond onlist so Doug and Nick can answer! If all you want > is thalamic volume then why do you have multiple comparisons? You only > have one number/subject, no? > Bruce > > On Thu, 11 Aug 2011, Knut J Bjuland wrote: > >> Hi Bruce >> >> I wish to use a group difference analysis using gender and correlate >> thalamus volume with IQ, and then apply multiple comparisons using FDR >> or Monte Carlo simulation. Do you have any links to a good tutorial? I >> inted to use mris_preproc and mris_glm for voulmetirc analysis, but I >> have some trouble figuring out --iv volmeasfile? >> >> Cheers >> Knut J >> >> >> Knut J >> >> On 08/11/2011 08:03 PM, Bruce Fischl wrote: >>> Hi Knut >>> >>> you don't need to register it since the segmentation (aseg) is created >>> from the same data as the surface. What kind of analysis are you >>> thinking of doing? >>> >>> cheers >>> Bruce >>> >>> >>> On Thu, 11 Aug 2011, Knut J Bjuland wrote: >>> >>>> I am working to do a volumetric analysis in Freesurfer using >>>> Thalamus. I >>>> do not know if this is the correct way to go. Should I first register >>>> thalamus to a surface using tkregister? There was also another post on >>>> this list, which suggested using tkregister2? I am also search to >>>> find >>>> a tutorial on how to create a volmask and the use it to calculate >>>> statistic in Freesurfer for Thalamus. >>>> >>>> Knut J >>>> >>>> _______________________________________________ >>>> 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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full flat patch issue
by francesca strappini 11 Aug '11

11 Aug '11

Hi, I'm trying to create a full flat map. The process of flattening seems has finished without any errors, but I got this error message when I tried to show up the full flat patch: lh.full.flat.patch.3d: face[0] = 0, but face 0 not in vertex 0 face list Thanks a lot Francesca

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tksurfer & rtview
by Michelle Umali 11 Aug '11

11 Aug '11

Dear Freesurfers, In an effort to figure out why my field sign data is a bunch of blue/red speckles, I looked at the polar and eccentricity maps separately on the surface. In both maps, I found that the values range from 0 to approximately 65. Does that seem to be OK, and if so, what do these numbers represent in terms of polar angle or eccentricity? Also, it seems that the color ranges in the overlay cannot show any values above 4; is there a way to visualize larger ranges (such as 0 to 65)? Thank you very much. Michelle

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Volumetric analysis of thalamus in freesurfer
by Knut J Bjuland 11 Aug '11

11 Aug '11

I am working to do a volumetric analysis in Freesurfer using Thalamus. I do not know if this is the correct way to go. Should I first register thalamus to a surface using tkregister? There was also another post on this list, which suggested using tkregister2? I am also search to find a tutorial on how to create a volmask and the use it to calculate statistic in Freesurfer for Thalamus. Knut J

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Fwd: Segmentation of hippocampal subfilelds
by mohan boddu 11 Aug '11

11 Aug '11

---------- Forwarded message ---------- From: mohan boddu <bmohan.boddu(a)gmail.com> Date: Tue, Aug 9, 2011 at 6:17 AM Subject: Re: [Freesurfer] Segmentation of hippocampal subfilelds To: Koen Van Leemput <koen(a)nmr.mgh.harvard.edu> Hello, I would like to thank you for the information, but the problem is, I am a CS student working on this and I dont have much idea about it. Basically my task is to convert those images into ROI mask. For this I have to follow the instructions in the website stated below: http://brainybehavior.com/neuroimaging/2010/06/saving-individual-labels-fro… But the process stated in the above website works for label maps, and if the images generated in the "*segmentation of hippocampal subfields*" ( http://www.freesurfer.net/fswiki/HippocampalSubfieldSegmentation) (8 images are generated for each side) stage are probability maps then what should be given as upper threshold(-uthr) and lower threshold(-thr) values. And as the last step says to divide it by its label number to normalize it. Is it necessary for the probability maps, if it is, then what would be the number that we have to divide? Sorry, if I am not clear and thank you very much for helping me out. On Tue, Aug 9, 2011 at 10:41 AM, Koen Van Leemput <koen(a)nmr.mgh.harvard.edu>wrote: > Hi Mohan, > > The segmentation results are given as probability maps: a (unsigned > 8-bit) value of 0 means probability 0 , 255 means probability 1, and > everything in between scales linearly. > > The proper way to obtain "crisp" label maps from these images is to > assign each voxel to the label map that has the highest probability, > so you'd need to read in all probabilty maps, visit each voxel and > compare the probabilities in the voxel for all structures. > > Generating such "scrisp", winner-takes-all label maps is not > recommended to calculate e.g., volumes etc, though... > > Hope this helps, > > Koen > > > On Mon, Aug 8, 2011 at 2:26 PM, mohan boddu <bmohan.boddu(a)gmail.com> > wrote: > > I have completed the segmentation of hippocampal subfileds, but now I > would > > like to know the generated images are in probability map or label map? If > > they are in label map what would be the best upper and lower thresholds > to > > generate the ROI mask images. Could you please also tell me the way to do > > so. > > > > -- > > --Mohan Boddu-- > > Research Assistant > > Department of Radiology and Imaging > > Research II Building > > Indiana University School Of Medicine > > Indiana University-Purdue University Indianapolis > > Indianapolis, IN 46202 > > > > > > _______________________________________________ > > 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. > > > > > -- --Mohan Boddu-- Research Assistant Department of Radiology and Imaging Research II Building Indiana University School Of Medicine Indiana University-Purdue University Indianapolis Indianapolis, IN 46202 -- --Mohan Boddu-- Research Assistant Department of Radiology and Imaging Research II Building Indiana University School Of Medicine Indiana University-Purdue University Indianapolis Indianapolis, IN 46202

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repeated measures ANOVA
by swoodman＠nmr.mgh.harvard.edu 11 Aug '11

11 Aug '11

Hello all, We would like to analyise our repeated measures DTI data using an ANOVA. We are wondering if someone might have experience running AVOVA's on 3D data? Is there a particular tool used or did you use MATLAB for this type of analysis? Thank you, Sandra Sandra Woodman Mood and Motor Control Laboratory Athinoula Martinos Center for Biomedical Imaging Massachusetts General Hospital

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mri_glmfit & .nii files
by Chindhuri Selvadurai 11 Aug '11

11 Aug '11

Hi freesurfers, I am trying to run an analysis right now, however, after using isxconcat, I am only finding ces.nii.gz files in the output directory and no .nii files. output dir: /cluster/manoach/milton/subjects/group_analysis/volume/m1 subjects_dir: /cluster/manoach/milton/subjects command: mri_glmfit --y /group_analysis/volume/m1/mstmct_v_base/type_v_rest/ces.nii.gz --glmdir group_analysis/volume/m1/ --osgm Not sure why this is the case.. any help would be appreciated! Thanks!

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: Memory and CPU Allocation?
by tapsya＠nmr.mgh.harvard.edu 11 Aug '11

11 Aug '11

Dear FSFAST, I am using the program selxavg3-sess on 3D data for a single session (i.e. selxavg3-sess -s avml07 -analysis $ana_vol -force) and it errors out with the following message: OLS Residual Pass run 1 t= 0.0 ??? Error using ==> unknown Out of memory. Type HELP MEMORY for your options. Error in ==> fast_selxavg3 at 469 rho1run = sum(rrun(1:end-1,:).*rrun(2:end,:))./rsserun; I am using FSFAST v 5.1. My analysis uses FIR design, 6 runs in each session with 18 contrasts. I executed the program on clusters 'launchpad' (@ Martino's center) and allocated 49GB to it. My question is how much CPU and memory you recommend I should allocate? I have also attached the log file in this email. Any help is greatly appreciated! Thanks. Wishes, Tapsya

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