Re: [Freesurfer] Cortical Thickness Zero Values
Hi Dr. Fischl and Dr. Greve, So moving the mouse over the medial wall seems to have all vertices within that to have a zero mm thickness as expected. The yellow outline is the lh.cortex.label and it seems to look good to me i.e. majority of the medial wall is properly masked. To be noted, this was the subject with 53 vertices labeled as 0s, which as you mentioned should be a substantial number. I am wondering what could be causing this? Lastly, I was wondering for cortical thickness analysis, is there a method to ensure the same number of vertices across all subjects with a corresponding mm thickness value. I have yet to try some commands, but preemptively I think if using mri_label2label with the trglabel lh.cortex.label as found in fsaverage directory and for each subject map their lh.cortex.label to fsaverage's lh.cortex.label and then from here I know I can run mris_anatomical_stats to extract average thickness, is there a command maybe using mris_convert with the label option to convert the label to the white surface and then using mris_convert with a -c option to have the scalar mm values corresponding to each vertex? or is this not a recommended approach? I would like ultimately import this into MATLAB to do some statistics and then view in freeview as a scalar overlay. Please advise. Thanks for the help, Taha On Tue, Oct 18, 2016 at 7:49 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu> wrote: > Hi Taha > > none that I can think of. The medial wall is pretty substantial region > though - I am more concerned about your subject with only 53 vertices in > it. You can visualize it by loading the ?h.cortex.label onto the inflated > surface. Everything not in the label should be set to 0 > > cheers > Bruce > > > > On Tue, 18 Oct 2016, Taha Abdullah wrote: > > I see now, thanks for the answer. If I may, is there any particular reason >> why such a disparity between >> two subjects, is this due to anatomical variability between individuals? >> I was surprised by the 9,000 >> values that was missing. >> >> On Fri, Oct 14, 2016 at 10:40 AM, Douglas Greve < >> gr...@nmr.mgh.harvard.edu> wrote: >> >> The entire medial wall has thickness values of 0 because there is >> no cortex there. There >> needs to be a surface in that area because we need a closed surface. >> >> >> On 10/12/16 8:10 PM, Taha Abdullah wrote: >> Hello All, >> Quick question, I ran recon-all with the qcache option and after >> converting the >> ?.thickness.fsaverage.mgh to an ascii text file via mri_convert I am >> noticing some vertices >> have 0mm thickness and it varies, for example, one subject had 53 >> vertices labeled as zeros >> while another had over 9,000 vertices. Is there a method I can use to >> have a thickness value >> for each of the 163000+ vertices? I am not sure if this is a possible >> registration issue to >> mni305. >> >> Thanks in advance, >> Taha >> -- >> Taha Abdullah >> Department of Physiology, >> Northwestern University Feinberg School of Medicine >> MS in Physiology and Biophysics, Georgetown University 2015 >> Work Cell: (312)-451-8468 >> >> >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> >> ___ >> Freesurfer mailing list >> Freesurfer@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. >> >> >> >> >> -- >> Taha Abdullah >> Department of Physiology, >> Northwestern University Feinberg School of Medicine >> MS in Physiology and Biophysics, Georgetown University 2015 >> Work Cell: (312)-451-8468 >> >> > ___ > Freesurfer mailing list > Freesurfer@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-m
Re: [Freesurfer] Cortical Thickness Zero Values
I see now, thanks for the answer. If I may, is there any particular reason why such a disparity between two subjects, is this due to anatomical variability between individuals? I was surprised by the 9,000 values that was missing. On Fri, Oct 14, 2016 at 10:40 AM, Douglas Greve <gr...@nmr.mgh.harvard.edu> wrote: > The entire medial wall has thickness values of 0 because there is no > cortex there. There needs to be a surface in that area because we need a > closed surface. > > On 10/12/16 8:10 PM, Taha Abdullah wrote: > > Hello All, > > Quick question, I ran recon-all with the qcache option and after > converting the ?.thickness.fsaverage.mgh to an ascii text file via > mri_convert I am noticing some vertices have 0mm thickness and it varies, > for example, one subject had 53 vertices labeled as zeros while another > had over 9,000 vertices. Is there a method I can use to have a thickness > value for each of the 163000+ vertices? I am not sure if this is a possible > registration issue to mni305. > > Thanks in advance, > Taha > -- > *Taha Abdullah* > *Department of Physiology,* > > *Northwestern University Feinberg School of Medicine * > *MS in Physiology and Biophysics, Georgetown University 2015* > *Work Cell: (312)-451-8468 <%28312%29-451-8468>* > > > ___ > Freesurfer mailing > listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > ___ > Freesurfer mailing list > Freesurfer@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. > > -- *Taha Abdullah* *Department of Physiology,* *Northwestern University Feinberg School of Medicine* *MS in Physiology and Biophysics, Georgetown University 2015* *Work Cell: (312)-451-8468* ___ Freesurfer mailing list Freesurfer@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] Cortical Thickness Zero Values
Hello All, Quick question, I ran recon-all with the qcache option and after converting the ?.thickness.fsaverage.mgh to an ascii text file via mri_convert I am noticing some vertices have 0mm thickness and it varies, for example, one subject had 53 vertices labeled as zeros while another had over 9,000 vertices. Is there a method I can use to have a thickness value for each of the 163000+ vertices? I am not sure if this is a possible registration issue to mni305. Thanks in advance, Taha -- *Taha Abdullah* *Department of Physiology,* *Northwestern University Feinberg School of Medicine* *MS in Physiology and Biophysics, Georgetown University 2015* *Work Cell: (312)-451-8468* ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] Projecting FA map onto fsaverge surface
Great! looks good, thanks for the help. Enjoy your weekend! On Fri, Aug 19, 2016 at 11:34 AM, Anastasia Yendiki < ayend...@nmr.mgh.harvard.edu> wrote: > > Hi Taha - Once you've mapped from the volume onto the white surface, you > should be able to display it on the inflated surface, and also to get > thickness statistics (thickness is just the distance between corresponding > points on the white and pial surface). You don't need to do anything to map > from white to inflated within an individual. > > Best, > a.y > > > On Fri, 19 Aug 2016, Taha Abdullah wrote: > > Excellent! Thank you for the quick advice, I tried this initially but I was >> using the wrong xfm format. >> Since I have the FA map in subject ?h.white space, I have done the same >> with the >> tract endings too. I am having some difficulties conceptually, in terms of >> projecting the end points onto either the subject specfic or >> fsaverage inflated >> surface. I assumed using mri_surf2surf would be sufficient to transform >> the >> endpts from subject surface ?h.white space to the inflated surface, but >> it is a >> scalar data file. Once the endpts are projected onto the inflated surface >> it >> seems straightforward to extract the thickness values for >> further analysis. >> Essentially replicating the attached image from Sølsnesa 2015. If you >> have any >> suggestions that would be much appreciated. Thank you very much! >> >> Best, >> Taha >> >> >> >> On Fri, Aug 19, 2016 at 9:49 AM, Anastasia Yendiki >> <ayend...@nmr.mgh.harvard.edu> wrote: >> >> Hi Taha - Trying getting a .dat registration file from bbregister >> and using that as the input to mri_vol2surf. There's a multimodal >> tutorial on the freesurfer wiki that might be of help. >> >> Best, >> a.y >> >> On Thu, 18 Aug 2016, Taha Abdullah wrote: >> >> Hello All, >> >> I am trying to project FA map (dtifit_FA.nii.gz) and the >> endpt[1/2].pd.nii.gz from TRACULA onto fsaverage surface >> space. >> I was following instructions on >> http://web.mit.edu/fsl_v5.0.8/fsl/doc/wiki/FDT(2f)UserGuide. >> html, >> under FreeSurfer >> Registration, to create the various xfms files. >> >> Next, I registered the FA map to subject conformed space >> using flirt >> * flirt -in dtifit_FA.nii.gz -ref >> ../../mri/orig.nii.gz -applyxfm -init >> ./xfms_taha/fa2freesurfer.mat -out fa2FS.nii.gz >> Then, I used mri_vol2surf to project the registered FA >> map onto fsaverage surface with the following command. >> * mri_vol2surf --mov fa2FS.nii.gz --projdist-max 6 6 1 >> --cortex --hemi rh --trgsubject fsaverage --regheader >> taha_brain >> --reg ./xfms_taha/fa2freesurfer.mat --o >> FA_2fsavg_surf.mgh >> Upon viewing in freeview the fsavg rh.white surface and >> fa2FS.nii.gz (FA map in FreeSurfer space) did not allign >> properly. I have tried some variations wtihout any luck. >> I used the following command line for freeview. >> * freeview -f/usr/local/freesurfer/subjec >> ts/fsaverage/surf/rh.white:overlay=FA_2fsavg_surf.m >> gh -v fa2FS.nii.gz >> * Attached are some pics of the FA confomred map and >> fsaverage.rh.white surface >> Do I need a xfm file for taliarch allignment? Any advice >> or insight would be greatly appreciated. >> >> Thanks in advance, >> Taha >> >> Terminal output: from mri_vol2surf >> srcvol = fa2FS.nii.gz >> srcreg = ./xfms_taha/fa2freesurfer.mat >> srcregold = 0 >> srcwarp unspecified >> surf = white >> hemi = rh >> trgsubject = fsaverage >> surfreg = sphere.reg >> ProjDist = 0.5 >> reshape = 0 >> interp = nearest >> float2int = round >> GetProjMax = 1 >> INFO: float2int code = 0 >> Done loading volume >> Computing registration from header. >> Using >> /usr/local/freesurfer/subjects/taha_brain/mri/orig.mgz >>
Re: [Freesurfer] Projecting FA map onto fsaverge surface
Excellent! Thank you for the quick advice, I tried this initially but I was using the wrong xfm format. Since I have the FA map in subject ?h.white space, I have done the same with the tract endings too. I am having some difficulties conceptually, in terms of projecting the end points onto either the subject specfic or fsaverage inflated surface. I assumed using mri_surf2surf would be sufficient to transform the endpts from subject surface ?h.white space to the inflated surface, but it is a scalar data file. Once the endpts are projected onto the inflated surface it seems straightforward to extract the thickness values for further analysis. Essentially replicating the attached image from Sølsnesa 2015. If you have any suggestions that would be much appreciated. Thank you very much! Best, Taha On Fri, Aug 19, 2016 at 9:49 AM, Anastasia Yendiki < ayend...@nmr.mgh.harvard.edu> wrote: > > Hi Taha - Trying getting a .dat registration file from bbregister and > using that as the input to mri_vol2surf. There's a multimodal tutorial on > the freesurfer wiki that might be of help. > > Best, > a.y > > On Thu, 18 Aug 2016, Taha Abdullah wrote: > > Hello All, >> >> I am trying to project FA map (dtifit_FA.nii.gz) and the >> endpt[1/2].pd.nii.gz from TRACULA onto fsaverage surface space. >> I was following instructions on http://web.mit.edu/fsl_v5.0.8/ >> fsl/doc/wiki/FDT(2f)UserGuide.html, under FreeSurfer >> Registration, to create the various xfms files. >> >> Next, I registered the FA map to subject conformed space using flirt >> * flirt -in dtifit_FA.nii.gz -ref ../../mri/orig.nii.gz -applyxfm -init >> ./xfms_taha/fa2freesurfer.mat -out fa2FS.nii.gz >> Then, I used mri_vol2surf to project the registered FA map onto fsaverage >> surface with the following command. >> * mri_vol2surf --mov fa2FS.nii.gz --projdist-max 6 6 1 --cortex --hemi >> rh --trgsubject fsaverage --regheader taha_brain >> --reg ./xfms_taha/fa2freesurfer.mat --o FA_2fsavg_surf.mgh >> Upon viewing in freeview the fsavg rh.white surface and fa2FS.nii.gz (FA >> map in FreeSurfer space) did not allign >> properly. I have tried some variations wtihout any luck. I used the >> following command line for freeview. >> * freeview -f >> /usr/local/freesurfer/subjects/fsaverage/surf/rh.white:overlay=FA_2fsavg_surf.mgh >> -v fa2FS.nii.gz >> * Attached are some pics of the FA confomred map and fsaverage.rh.white >> surface >> >> Do I need a xfm file for taliarch allignment? Any advice or insight would >> be greatly appreciated. >> >> Thanks in advance, >> Taha >> >> Terminal output: from mri_vol2surf >> srcvol = fa2FS.nii.gz >> srcreg = ./xfms_taha/fa2freesurfer.mat >> srcregold = 0 >> srcwarp unspecified >> surf = white >> hemi = rh >> trgsubject = fsaverage >> surfreg = sphere.reg >> ProjDist = 0.5 >> reshape = 0 >> interp = nearest >> float2int = round >> GetProjMax = 1 >> INFO: float2int code = 0 >> Done loading volume >> Computing registration from header. >> Using /usr/local/freesurfer/subjects/taha_brain/mri/orig.mgz as target >> reference. >> Loading label /usr/local/freesurfer/subjects/fsaverage/label/rh.cortex. >> label >> Reading surface /usr/local/freesurfer/subjects/taha_brain/surf/rh.white >> Done reading source surface >> Mapping Source Volume onto Source Subject Surface >> 1 6 6 6 >> using old >> Done mapping volume to surface >> Number of source voxels hit = 81606 >> Reading source surface registration >> /usr/local/freesurfer/subjects/taha_brain/surf/rh.sphere.reg >> Done loading source registration surface >> Reading target registration >>/usr/local/freesurfer/subjects/fsaverage/surf/rh.sphere.reg >> Done loading target registration surface >> Mapping Surfaces (taha_brain -> fsaverage) >> surf2surf_nnfr: building source hash (res=16). >> Surf2Surf: Forward Loop (163842) >> >> surf2surf_nnfr: building target hash (res=16). >> Surf2Surf: Reverse Loop (143161) >> Reverse Loop had 26084 hits >> Surf2Surf: Dividing by number of hits (163842) >> INFO: nSrcLost = 0 >> Done mapping surfaces >> nSrc121 = 107182, nSrcLost = 0, nSrcMulti = 35979, MnSrcMultiHits = >> 2.29979 >> nTrg121 = 142955, nTrgMulti = 20887, MnTrgMultiHits = 2.24882 >> Masking with /usr/local/freesurfer/subjects/fsaverage/label/rh.cortex. >> label >> Writing to FA_2fsavg_surf.mgh >> Dim: 163842 1 1 >> >> >> -- >> Taha Abdullah >> Department of Physiology >> Northwestern Unive
[Freesurfer] Seed based volume output to surface
Good Afternoon Freesurfers, I am running a seed-based connectivity for one individual subject. The seed is in the L_parahippocampus. I have followed the steps outlined in FSFast walkthrough. Below is a list of my commands. Mind you that I was trying to keep my analysis as simple as possible before delving deeper into it. I have a question on the sig.nii.gz output. Please see at the end. preproc-sess -s taha_brain -fwhm 0 -surface self lhrh -mni305-2mm -fsd resting_scans -per-run fcseed-config -segid 1016 -fcname L_parahipp -fsd resting_scans -mean -cfg mean.L_parahipp.config -overwrite -fillthresh 1 fcseed-sess -s taha_brain -cfg mean.L_parahipp.config mkanalysis-sess -analysis L_parahipp_seed.surf.lh -surface self lh -fwhm 0 -notask -taskreg L_parahipp 1 -fsd resting_scans -TR 0.555 -mcextreg -polyfit 2 -per-run selxavg3-sess -s taha_brain -a L_parahipp_seed.surf.lh Output files /home/tabdullah/Project/Sess01/fsd/L_parahipp_seed.surf.lh/L_parahipp/sig.nii.gz amongst others *Is there a way to convert the volume to a surface and then extract per vertex the sig value?* I used tmri_vol2surf see below: mri_vol2surf --mov ./sig.nii.gz --reg /home/tabdullah/resting_state_1/taha_brain/resting_scans/001/register.dof6.dat --trgsubject taha_brain --interp nearest --projfrac 0.5 --hemi lh --o /home/tabdullah/sig.mgh --noreshape --cortex I tried using mris_convert -c mris_convert -c ./sig.mgh /usr/local/freesurfer/subjects/taha_brain/surf/lh.white sig.asc The last column is all zeros. I am not entirely sure what I am doing wrong here, it is probably somewhere in the last two commands. Possibly using mri_segstats or mri_read.m? Any help would be greatly appreciated. Apologize in advance for the long email. -- Taha Abdullah Department of Physiology Northwestern University Feinberg School of Medicine Masters of Science Physiology and Biophysics, Georgetown University 2015 Work: (312)-503-0413 ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] Extracting BOLD from a flattened surface
Hello Freesurfer Team,
Sorry for being so late with this message I was trying different things to
accomplish extracting BOLD values from a flattened surface. I followed the
overall instructions on this website
http://web.mit.edu/fsl_v5.0.8/fsl/doc/wiki/FreeSurfer.html. I have the
flattened patch from tksurfer and I want to conduct a rsfMRI analysis on a
flattened patch from a feat directory. Do you have any recommendations on
the proper workflow? I believe that I need to run
mri_label2vol --annot /path to subj/label/lh.aparc.annot --temp
func4d.nii.gz --reg (output from reg-feat2anat) --o myoutput --hemi lh
--subject --proj 0 1 .1
The output has similar dimensions as functional and it is only cortical
areas but the time dimensions are no longer there. Not sure how to actually
extract the bold signal, maybe something with mri_segstats? And I think it
will be straightforward to understand the spatial changes occurring during
flattening since vertex identity stays the same and can be read in MATLAB,
correct? Please let me know at your earliest convenience.
Best,
Taha
On Thu, May 5, 2016 at 9:21 AM, Douglas Greve <gr...@nmr.mgh.harvard.edu>
wrote:
> So you have 1 column, but you want 1 column for each vertex? We don't have
> anything to do that, but you can do it in matlab, eg,
> M = fast_vol2mat(MRIread('lh.yourdata.mgh'));
> M will be a 240x127000 matrix
>
>
> On 5/4/16 8:36 PM, Taha Abdullah wrote:
>
> Hello Doug,
>
> Sorry for the confusing and long email, I am interested in extracting the
> raw BOLD signal from a processed 4D nifit file. After registering the
> functional to ${subject}/mri/orig.mgz and generating the registration file,
> I proceeded to convert the functional image to the same dimensions as
> the lh.inflated surface via mri_vol2surf so the functional data image now
> has 127000 x 1 x 1 x 240. So I ran mri_segstats command to extract the bold
> signal, but I ended up having 240 rows and 1 column in the text file...the
> ultimate goal is to quantify the wave propagation of the BOLD time series
> across a flattened patch. Any advice would be greatly appreciated.
>
> Thanks!
>
> On Wed, May 4, 2016 at 2:26 PM, Douglas N Greve <gr...@nmr.mgh.harvard.edu
> > wrote:
>
>>
>> Sorry, can you tell me what you are trying to do? You just want a number
>> of time points -by- number of vertices file? Then mri_vol2surf should do
>> that for you. Flattening is irrelevant for this as it only changes the
>> xyz coordinate of the vertex and not the vertex identity.
>> doug
>>
>>
>> On 04/29/2016 11:24 AM, Taha Abdullah wrote:
>> > Hello Freesurfer Experts,
>> >
>> > Long story short--I would like to extract BOLD values from each TR
>> > across all vertices for one subjects flattened surface
>> > Following is a brief overview of my steps and at the end you can see
>> > where I am stuck.
>> > First, after */recon-all /I* followed the steps to cut the lh inflated
>> > surface, saved as a patch, ran /*mris_flatten, */converted patch into
>> > asc file.
>> > Second, I used read_patch.m to extract all spatial information and a
>> > net loss of approximately 10k vertices (127k to 116k)
>> >
>> > We had all functional images processed in FSL, the 4D file has
>> > 64x64x36x240 dimensions (voxels are 3.4x3.4x3.0). Next, co-registered
>> > the functional and anatomicals together via the following cmd:
>> > */ bbregister --s cbp001_v1 --mov filtered_func_data.nii.gz --bold
>> > --init-fsl --reg dummy1.da/*t. Afterwards, converted the volume to a
>> > surface using the following cmd*/: mri_vol2surf --mov
>> > filtered_func_data.nii.gz --reg dummy1.dat --projfrac 0.5 --interp
>> > trilinear --hemi lh --o ./lh.func.vol2surf.mgh. /*THe dimensions are
>> > 127027 x 1 x 1 x 240. Visually no problem when using*/ tksurfer
>> > cbp001_v1 lh inflated -patch /path to flattened patch/ -overlay
>> > /lh.func.vol2surf.mgh/ -timecourse lh.func.vol2surf.mgh;/* click on
>> > the patch and shows the timecourse for that selected vertex. Using the
>> > View>Configure>overlay I can shuffle through the TRs to inspect the
>> > change in raw BOLD signal per vertex.
>> >
>> > I have been perusing the email web server searching for how to extract
>> > the hemodynamic waveform for each vertex across the flattened surface
>> > and ultimately will be using matlab to understand how the spatial
>> > transformation is happening. As well I have all the matlab files that
>> > seemed relevant to my query (read_surf.m, read_patch.m, and
>> > readMRI.m). I was hoping that I would be able to have a text fi
Re: [Freesurfer] Extracting BOLD from a flattened surface
Hello Doug,
Sorry for the confusing and long email, I am interested in extracting the
raw BOLD signal from a processed 4D nifit file. After registering the
functional to ${subject}/mri/orig.mgz and generating the registration file,
I proceeded to convert the functional image to the same dimensions as
the lh.inflated surface via mri_vol2surf so the functional data image now
has 127000 x 1 x 1 x 240. So I ran mri_segstats command to extract the bold
signal, but I ended up having 240 rows and 1 column in the text file...the
ultimate goal is to quantify the wave propagation of the BOLD time series
across a flattened patch. Any advice would be greatly appreciated.
Thanks!
On Wed, May 4, 2016 at 2:26 PM, Douglas N Greve <gr...@nmr.mgh.harvard.edu>
wrote:
>
> Sorry, can you tell me what you are trying to do? You just want a number
> of time points -by- number of vertices file? Then mri_vol2surf should do
> that for you. Flattening is irrelevant for this as it only changes the
> xyz coordinate of the vertex and not the vertex identity.
> doug
>
>
> On 04/29/2016 11:24 AM, Taha Abdullah wrote:
> > Hello Freesurfer Experts,
> >
> > Long story short--I would like to extract BOLD values from each TR
> > across all vertices for one subjects flattened surface
> > Following is a brief overview of my steps and at the end you can see
> > where I am stuck.
> > First, after */recon-all /I* followed the steps to cut the lh inflated
> > surface, saved as a patch, ran /*mris_flatten, */converted patch into
> > asc file.
> > Second, I used read_patch.m to extract all spatial information and a
> > net loss of approximately 10k vertices (127k to 116k)
> >
> > We had all functional images processed in FSL, the 4D file has
> > 64x64x36x240 dimensions (voxels are 3.4x3.4x3.0). Next, co-registered
> > the functional and anatomicals together via the following cmd:
> > */ bbregister --s cbp001_v1 --mov filtered_func_data.nii.gz --bold
> > --init-fsl --reg dummy1.da/*t. Afterwards, converted the volume to a
> > surface using the following cmd*/: mri_vol2surf --mov
> > filtered_func_data.nii.gz --reg dummy1.dat --projfrac 0.5 --interp
> > trilinear --hemi lh --o ./lh.func.vol2surf.mgh. /*THe dimensions are
> > 127027 x 1 x 1 x 240. Visually no problem when using*/ tksurfer
> > cbp001_v1 lh inflated -patch /path to flattened patch/ -overlay
> > /lh.func.vol2surf.mgh/ -timecourse lh.func.vol2surf.mgh;/* click on
> > the patch and shows the timecourse for that selected vertex. Using the
> > View>Configure>overlay I can shuffle through the TRs to inspect the
> > change in raw BOLD signal per vertex.
> >
> > I have been perusing the email web server searching for how to extract
> > the hemodynamic waveform for each vertex across the flattened surface
> > and ultimately will be using matlab to understand how the spatial
> > transformation is happening. As well I have all the matlab files that
> > seemed relevant to my query (read_surf.m, read_patch.m, and
> > readMRI.m). I was hoping that I would be able to have a text file with
> > all the vertices (127K not the flattened 116k) in rows and each column
> > would have the TRs; I ran this command;*/ mri_segstats --slabel
> > cbp001_v1 lh
> > /home/share/freesurfer/subjects/cbp001_v1/label/lh.cortex.label
> > --avgwf mri_seg_stats.dat --i lh.func.vol2surf.mgh/*, output was the
> > 240 TRs as rows and seems like the average global BOLD signal in the
> > single column corresponding with each TR. Excuse my naiveness, I just
> > recently (1 month ago) started using freesurfer and I feel like I have
> > exhausted as much of the information available on the FS wiki and
> > email server. Any information or advice would be great! I put the
> > commands just to give an idea of my workflow (most of the command
> > lines are from the email server or the FS Wiki) and if there are any
> > issues with my steps please let me know so I can correct them before
> > starting the group analysis.
> >
> > Best,
> > Taha
> >
> > --
> > Taha Abdullah
> > Department of Physiology
> > Northwestern University
> > Masters of Science Physiology and Biophysics, Georgetown University 2015
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
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Re: [Freesurfer] Recon-all -subcortseg finished with error
I found the option here < http://surfer.nmr.mgh.harvard.edu/docs/recon-all.help.txt> And out of curiosity, I ran autorecon 1 followed by -subcort-seg then mri_segstats and see how large the difference is and using the faster computational approach most of the subcortical ROI volumes were slightly underestimated. We have about 500 T1s is the reason for using the faster computational approach, it is evident there are going to be differences...for the time being we will most like try to run recon-all with the surfaces and using as many different options to speed it up. Thanks for the help! On Sun, May 1, 2016 at 11:46 AM, Bruce Fischl <fis...@nmr.mgh.harvard.edu> wrote: > what is -nosphere? I don't think it'sa recon-all option, is it? > > I guess I would recommend running things all the way through unless you > really don't have the compute time/disk space > > cheers > Bruce > > > > > On Sun, 1 May 2016, Taha Abdullah wrote: > > Hello Burce, >> Thank you for the reply, I see well I would want to use the surfaces then. >> Would you recommend something like running recon-all and using -nosphere? >> >> -Taha >> >> On Sat, Apr 30, 2016 at 1:14 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu >> > >> wrote: >> Hi Taha >> >> you can, but it won't be as accurate since the surfaces give >> better estimates of cortex and such (and we use them to >> automatically correct the aseg). You can run the individual >> steps through the end of mri_ca_label if you want to stop there >> >> cheers >> Bruce >> >> On Fri, 29 Apr 2016, Taha Abdullah wrote: >> >> Hello All, >> I am running an analysis strictly on subcortical >> volumes, and to save time >> and disk space I wanted to avoid if possible >> construction of surfaces and >> seems that it is necessary? I first ran recon-all >> -autorecon1, second I ran >> recon-all -subcortseg and the final error was >> regarding no such file or >> dir, specifically the /surf/lh.white. >> >> Is there a better way to run this type of analysis >> to save disk space and >> time? Possibly using -autorecon2'; would love any >> input. Thank you in >> advance! >> >> -- >> Taha Abdullah >> Department of Physiology >> Northwestern University >> Masters of Science Physiology and Biophysics, >> Georgetown University 2015 >> >> >> ___ >> Freesurfer mailing list >> Freesurfer@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. >> >> >> >> >> -- >> Taha Abdullah >> Department of Physiology >> Northwestern University >> Masters of Science Physiology and Biophysics, Georgetown University 2015 >> >> > ___ > Freesurfer mailing list > Freesurfer@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. > > -- Taha Abdullah Department of Physiology Northwestern University Masters of Science Physiology and Biophysics, Georgetown University 2015 ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] Recon-all -subcortseg finished with error
Hello Burce, Thank you for the reply, I see well I would want to use the surfaces then. Would you recommend something like running recon-all and using -nosphere? -Taha On Sat, Apr 30, 2016 at 1:14 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu> wrote: > Hi Taha > > you can, but it won't be as accurate since the surfaces give better > estimates of cortex and such (and we use them to automatically correct the > aseg). You can run the individual steps through the end of mri_ca_label if > you want to stop there > > cheers > Bruce > > > On Fri, 29 Apr 2016, Taha Abdullah wrote: > > Hello All, >> I am running an analysis strictly on subcortical volumes, and to save time >> and disk space I wanted to avoid if possible construction of surfaces and >> seems that it is necessary? I first ran recon-all -autorecon1, second I >> ran >> recon-all -subcortseg and the final error was regarding no such file or >> dir, specifically the /surf/lh.white. >> >> Is there a better way to run this type of analysis to save disk space and >> time? Possibly using -autorecon2'; would love any input. Thank you in >> advance! >> >> -- >> Taha Abdullah >> Department of Physiology >> Northwestern University >> Masters of Science Physiology and Biophysics, Georgetown University 2015 >> >> > ___ > Freesurfer mailing list > Freesurfer@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. > > -- Taha Abdullah Department of Physiology Northwestern University Masters of Science Physiology and Biophysics, Georgetown University 2015 ___ Freesurfer mailing list Freesurfer@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] Recon-all -subcortseg finished with error
Hello All, I am running an analysis strictly on subcortical volumes, and to save time and disk space I wanted to avoid if possible construction of surfaces and seems that it is necessary? I first ran recon-all -autorecon1, second I ran recon-all -subcortseg and the final error was regarding no such file or dir, specifically the /surf/lh.white. Is there a better way to run this type of analysis to save disk space and time? Possibly using -autorecon2'; would love any input. Thank you in advance! -- Taha Abdullah Department of Physiology Northwestern University Masters of Science Physiology and Biophysics, Georgetown University 2015 ___ Freesurfer mailing list Freesurfer@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.
