Freesurfer

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30132 discussions

Brodmann areas stats table
by _andreia_＠sapo.pt 11 Aug '11

11 Aug '11

FreeSurfers, Is there a way to get BA cortical thickness in a table to export from FS? As there is for aseg and aparc stats. Thanks! Andreia -- Andreia Pereira, MSc student Visual Neuroscience Laboratory IBILI-Faculdade de Medicina Azinhaga de Santa Comba 3000-354 Coimbra Portugal Phone +(351) 239480220 Fax +(351) 239480280

2 1

Re: [Freesurfer] Volumetric analysis of thalamus in freesurfer
by Douglas N Greve 11 Aug '11

11 Aug '11

I'm not sure what you would visualize. These are just single numbers per subject. doug Knut J Bjuland wrote: > Hi > > Is is possible to visualize this data on sub-cortical structure in wya > similar to the aging tutorial? > > Knut J > > On 08/11/2011 09:03 PM, Douglas N Greve wrote: > >> use --segno 10 --segno 49 >> These codes are from $FREESURFER_HOME/FreeSurferColorLUT.txt and >> correspond to left and right thalamus. Use -m volume to get the volume >> of thalamus (this is the default). If you're only looking at one >> measure, then no correction for multiple comparisons is necessary. You >> can test the effect of gender by loading this output into a stats >> program or using mri_glmfit with the --table option. >> doug >> >> Knut J Bjuland wrote: >> >>> 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. >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>> >>>>> >>>> >>>> >>> _______________________________________________ >>> 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

1 0

tksurfer & rtview
by Michelle Umali 11 Aug '11

11 Aug '11

Hi Doug, The z-values are consistently near or greater than 4. It just seems that the visualization of the angles is somehow incorrect... Is there be anything else that I need to check? Thanks. Michelle

2 3

registration issues with lesioned brains and kids' brains
by Catherine Wan 11 Aug '11

11 Aug '11

Dear Freesurfer-list, I have 2 questions: one regarding lesioned brains and another regarding kids’ brains. 1) All of our patients have large lesions on the left side. After the recon-all step, I used tkmedit brainmask.mgz and found that for some patients, the lesion location had been flipped from left to right (see attached). Any suggestions on how to solve this issue, prior to running a group level analysis? 2) We have preprocessed some images of typically-developing children (9-11yo). After recon-all, I checked the registration using tkregister2 --mgz –s --fstal --surf orig and found that the green line didn’t cover the surfaces well in most cases (see attached) . I’ve read in previous postings that Freesurfer should be fine with kids’ brains, so perhaps we don't need to modify them manually? Is there any other way to check for registration? Any other suggestions? Many thanks in advance for your help! Regards, Catherine

2 4

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.

2 5

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? > > >

1 0

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. >>> >>> >>> >> >> >> > >

2 1

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

2 1

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

2 3

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

2 1

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