[Freesurfer] tracula -bedp - path
Hi, I ran into 2 problems related to tracula. 1. trac-all -bedp command exits with following message. WARN: Running FSL's bedbost locally - this might take a while WARN: It is recommended to run this step on a cluster bedpostx_seychelles /usr/local/freesurfer/subjects/C001/dmri subjectdir is /usr/local/freesurfer/subjects/C001/dmri Making bedpostx directory structure Queuing preprocessing stages [: 223: NONE: unexpected operator [: 314: NONE: unexpected operator [: 327: xbedpostx_pre: unexpected operator [: 486: x: unexpected operator [: 486: -le: argument expected Queuing parallel processing stage [: 223: NONE: unexpected operator [: 327: xbedpostx: unexpected operator [: 486: x53: unexpected operator 0 slices processed Queuing post processing stage [: 223: NONE: unexpected operator [: 314: NONE: unexpected operator [: 327: xbedpostx_post: unexpected operator [: 486: x: unexpected operator [: 486: -le: argument expected This problem has been posted in May and June. bedpostx from command line runs perfectly and that is how I have been running it so far. One of u suggested to try the following: /usr/local/fsl/bin/bedpostx_single_slice.sh /disks/open/judit/subjects/diffusion_tutorial/dtisubjects2005/subj_523/dmri 2 1 1000 1250 25 1 0 then I got: ** ERROR (nifti_image_read): failed to find header file for '/disks/open/judit/subjects/diffusion_tutorial/dtisubjects2005/subj_523/dmri/data_slice_' ** ERROR: nifti_image_open(/disks/open/judit/subjects/diffusion_tutorial/dtisubjects2005/subj_523/dmri/data_slice_): bad header info ERROR: failed to open file /disks/open/judit/subjects/diffusion_tutorial/dtisubjects2005/subj_523/dmri/data_slice_ ERROR: Could not open image /disks/open/judit/subjects/diffusion_tutorial/dtisubjects2005/subj_523/dmri/data_slice_ Image Exception : #22 :: Failed to read volume /disks/open/judit/subjects/diffusion_tutorial/dtisubjects2005/subj_523/dmri/data_slice_ An exception has been thrown Failed to read volume /disks/open/judit/subjects/diffusion_tutorial/dtisubjects2005/subj_523/dmri/data_slice_Trace: read_volume4DROI. Done Can u suggest a reason behind all this? This happens on Linux machine (2.6.35-28-generic #50-Ubuntu 10.10, x86_64, Java VM Version: Java 1.6.0_17-b04 with Sun Microsystems Inc. Java HotSpot(TM) 64-Bit Server VM mixed mode). On Mac OS X (version 10.7.1 - Lion, 2 x 2.66 GHz 6-core Intel Xeon processors, 32 GB 1333 MHz DDR3 RAM) trac-all -bedp runs well. My other question is: trac-all -path exists with error (in case of a single subject): Loading DWIs from /disks/open/judit/subjects/diffusion_tutorial/dtisubjects2005/subj_501/dmri/dwi.nii.gz Loading mask from /disks/open/judit/subjects/diffusion_tutorial/dtisubjects2005/subj_501/dlabel/diff/aparc+aseg_mask.bbr.nii.gz Loading BEDPOST parameter samples from /disks/open/judit/subjects/diffusion_tutorial/dtisubjects2005/subj_501/dmri.bedpostX Loading segmentation map from /disks/open/judit/subjects/diffusion_tutorial/dtisubjects2005/subj_501/dlabel/mni/aparc+aseg.nii.gz Loading b-values from /disks/open/judit/subjects/diffusion_tutorial/dtisubjects2005/subj_501/dmri/bvals Loading gradients from /disks/open/judit/subjects/diffusion_tutorial/dtisubjects2005/subj_501/dmri/bvecs Segmentation fault Linux Odd 2.6.35-28-generic #50-Ubuntu SMP Fri Mar 18 18:42:20 UTC 2011 x86_64 GNU/Linux trac-paths exited with ERRORS at Fri Oct 7 10:21:20 CEST 2011 thanks for help. Judit ___ 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] warped flat occip patches and fieldsign maps
Hi Michelle, the odd shaped shards and triangles usually means you recreated the surfaces after flattening, so the flattening needs to be redone. The swirls can be a number of things, possibly incorrect cuts. If you want to upload an example I'll take a look. cheers Bruce On Thu, 6 Oct 2011, Michelle Umali wrote: Dear freesurfers, I've been analyzing my retinotopy , have finally been able to run fieldsign-sess without running into dimension mismatch errors. Everything seemed ok until I tried looking at the fieldsign maps on flat patches. Some patches are warped with odd out of plane swirls. In others, all i get are odd shaped shards and triangles. What might be the cause? thanks, Michelle ___ 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] question about contrast file during group analysis with command line
Hi all : I'm performing general linear model (GLM) analysis in the surface,the attachments above are FSGD file and contrast files(the last three attachments).i wonder if my contrast files are correct. the attachment named diff-C-H-thickness.txt is about difference between C and H and the last two are about difference between C and p and difference between P and H,Here,C H and P represent three groups Any suggestions appreciatedGroupDescriptorFile 1 Title genderage MeasurementName thickness Class C-Male Class C-Female Class P-Male Class P-Female Class H-Male Class H-Female Variables age Input chen_haoC-Female20 Input cui_xi_long C-Female23 Input jiang_xue C-Female24 Input li_qing_jingC-Female24 Input li_ru C-Male 22 Input li_teng_yu C-Male 21 Input liao_yun_feng C-Male 24 Input long_hu C-Male 29 Input long_zhiC-Male 26 Input lv_hai_long C-Male 23 Input peng_chend C-Male 24 Input yue_zhong_wei C-Male 22 Input zhang_qian C-Male 25 Input zhao_ke C-Male 27 Input zhu_min C-Male 21 Input cai_rongP-Female23 Input chen_guo_wu P-Male 23 Input huang_din_qiang P-Male 22 Input kong_fang_fang P-Female24 Input li_guang_yaoP-Male 24 Input liu_zheng_hua P-Male 26 Input long_binP-Male 29 Input qiu_hao P-Male 21 Input quan_su_bin P-Male 22 Input wu_jian_nongP-Male 25 Input wu_li_hui P-Female20 Input xiao_qiao_ling P-Female24 Input xie_gangP-Male 21 Input xu_xian P-Male 24 Input zhang_hai_tao P-Male 27 Input chen_guo_wenH-Male 23 Input chen_hong_liang H-Male 24 Input chen_lu_hua H-Female24 Input kong_san_jian H-Male 21 Input li_you_quan H-Male 21 Input liu_bin H-Male 25 Input long_feng_boH-Male 27 Input qiu_yi H-Male 24 Input tan_zhi_hui H-Male 22 Input wu_xiao_jun H-Male 29 Input wu_yao H-Female20 Input xiao_zhi_ping H-Female23 Input xie_yi_long H-Female24 Input zhi_hui_tao H-Male 26 Input zhou_wei_huaH-Male 22 +1 +1 0 0 -1 -1 0 0 0 0 0 0+1 +1 -1 -1 0 0 0 0 0 0 0 00 0 +1 +1 -1 -1 0 0 0 0 0 0___ 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] tracula -bedp - path
Hi Judit, 1. If you can run bedpostx directly then you should do: bedpostx /usr/local/freesurfer/subjects/C001/dmri Note that this dmri directory and the one you tried to run bedpostx_single_slice.sh on are different, so I'm not sure which location is the right one where your data is, but in any case you don't need to run bedpostx_single_slice.sh. 2. The error seems to occur either when it's reading the bvecs file, or right after that when it's accessing the bedpostx outputs. So I'd try to look those for that subject and see if everything is ok. Hope this helps, a.y On Fri, 7 Oct 2011, Judit Haasz wrote: Hi, I ran into 2 problems related to tracula. 1. trac-all -bedp command exits with following message. WARN: Running FSL's bedbost locally - this might take a while WARN: It is recommended to run this step on a cluster bedpostx_seychelles /usr/local/freesurfer/subjects/C001/dmri subjectdir is /usr/local/freesurfer/subjects/C001/dmri Making bedpostx directory structure Queuing preprocessing stages [: 223: NONE: unexpected operator [: 314: NONE: unexpected operator [: 327: xbedpostx_pre: unexpected operator [: 486: x: unexpected operator [: 486: -le: argument expected Queuing parallel processing stage [: 223: NONE: unexpected operator [: 327: xbedpostx: unexpected operator [: 486: x53: unexpected operator 0 slices processed Queuing post processing stage [: 223: NONE: unexpected operator [: 314: NONE: unexpected operator [: 327: xbedpostx_post: unexpected operator [: 486: x: unexpected operator [: 486: -le: argument expected This problem has been posted in May and June. bedpostx from command line runs perfectly and that is how I have been running it so far. One of u suggested to try the following: /usr/local/fsl/bin/bedpostx_single_slice.sh/disks/open/judit/subjects/diffusion_tutorial/dtisubjects2005/subj_523/dmri 2 1 1000 1250 25 1 0 then I got: ** ERROR (nifti_image_read): failed to find header file for'/disks/open/judit/subjects/diffusion_tutorial/dtisubjects2005/subj_523/dmr i/data_slice_' ** ERROR:nifti_image_open(/disks/open/judit/subjects/diffusion_tutorial/dtisubjects2 005/subj_523/dmri/data_slice_): bad header info ERROR: failed to open file/disks/open/judit/subjects/diffusion_tutorial/dtisubjects2005/subj_523/dmri /data_slice_ ERROR: Could not open image/disks/open/judit/subjects/diffusion_tutorial/dtisubjects2005/subj_523/dmri /data_slice_ Image Exception : #22 :: Failed to read volume/disks/open/judit/subjects/diffusion_tutorial/dtisubjects2005/subj_523/dmri /data_slice_ An exception has been thrown Failed to read volume/disks/open/judit/subjects/diffusion_tutorial/dtisubjects2005/subj_523/dmri /data_slice_Trace: read_volume4DROI. Done Can u suggest a reason behind all this? This happens on Linux machine (2.6.35-28-generic #50-Ubuntu 10.10, x86_64, Java VM Version: Java 1.6.0_17-b04 with Sun Microsystems Inc. Java HotSpot(TM) 64-Bit Server VM mixed mode). On Mac OS X (version 10.7.1 - Lion, 2 x 2.66 GHz 6-core Intel Xeon processors, 32 GB 1333 MHz DDR3 RAM) trac-all -bedp runs well. My other question is: trac-all -path exists with error (in case of a single subject): Loading DWIs from/disks/open/judit/subjects/diffusion_tutorial/dtisubjects2005/subj_501/dmri /dwi.nii.gz Loading mask from/disks/open/judit/subjects/diffusion_tutorial/dtisubjects2005/subj_501/dlab el/diff/aparc+aseg_mask.bbr.nii.gz Loading BEDPOST parameter samples from/disks/open/judit/subjects/diffusion_tutorial/dtisubjects2005/subj_501/dmri .bedpostX Loading segmentation map from/disks/open/judit/subjects/diffusion_tutorial/dtisubjects2005/subj_501/dlab el/mni/aparc+aseg.nii.gz Loading b-values from/disks/open/judit/subjects/diffusion_tutorial/dtisubjects2005/subj_501/dmri /bvals Loading gradients from/disks/open/judit/subjects/diffusion_tutorial/dtisubjects2005/subj_501/dmri /bvecs Segmentation fault Linux Odd 2.6.35-28-generic #50-Ubuntu SMP Fri Mar 18 18:42:20 UTC 2011 x86_64 GNU/Linux trac-paths exited with ERRORS at Fri Oct 7 10:21:20 CEST 2011 thanks for help. Judit ___ 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] Resampling NIFTI images
Dear FreeSurfers, This is a question I posted yesterday and I got not answer yet. I am trying to re-sample a NIFTI image (obtained after MRIcron conversion, from a dcm image) in Freesurfer with a scale factor of 2. I know about mri_convert with the option -rt but this doesn't give me any option for the scale factor (for e.g. I want to drop each second slice from my NIFTI image). Any suggestion will be greatly appreciated. Thank you. AK ___ 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 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] Resampling NIFTI images
Hi Antonella, this would be pretty easy to do in matlab I guess. Why do you want to do it? Do you really just want to drop every other slice? Do you want to change the in-plane resolution? Bruce On Fri, 7 Oct 2011, Antonella Kis wrote: Dear FreeSurfers, This is a question I posted yesterday and I got not answer yet. I am trying to re-sample a NIFTI image (obtained after MRIcron conversion, from a dcm image) in Freesurfer with a scale factor of 2. I know about mri_convert with the option -rt but this doesn't give me any option for the scale factor (for e.g. I want to drop each second slice from my NIFTI image). Any suggestion will be greatly appreciated. Thank you. AK ___ 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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Process monkey data
I have data from 100 monkeys and I need to compare cortical thickness among two groups. In the wiki page there is an entry MonkeyData that has a set of scripts which break-down the steps needed, unfortunately I'm having trouble with this scripts and FS 5.1 Are there an updated version of those procedures? Thanks PPJ -- iOS 5.0 ___ 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] Process monkey data
Hi Pedro, On Oct 7, 2011, at 9:02 , Pedro Paulo de Magalhães Oliveira Junior wrote: I have data from 100 monkeys and I need to compare cortical thickness among two groups. In the wiki page there is an entry MonkeyData that has a set of scripts which break-down the steps needed, unfortunately I'm having trouble with this scripts and FS 5.1 I was somewhat involved with these scripts in the past, I only used them with 4.5 so far, therefore I do not know what issues you encounter, care to elaborate what causes the trouble? (BTW the old monkey pipeline will fake the resolution information in the volume headers so Freesurfer sees 1mm isotropic and does not go and resamples the data to 1mm, at least for macaques and smaller monkeys that would throw away too much information in my opinion (don't know for apes...)). So if you use these scripts for morphometry keep in mind that all length measurements are off by 1/real_isotropic_voxel_size, area and volume are therefore off as well; but then this can be easily corrected for I think... Now, I hope some other monkey people can chime in and share their improved freesurfer pipeline :) Best Sebastian Are there an updated version of those procedures? Thanks PPJ -- iOS 5.0 ___ 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. -- Sebastian Moeller telephone: +1-626-325-8598 /+1-626-395-6523 / +1-626-395-6616 fax: 626-395-8826 German GSM: +49 - 15 77 - 1 90 31 41 mobile: +1-626-325-8598 +1-626-807-5242 US CDMA: +1-626-807-5242 moel...@caltech.edu Division of Biology MC 114-96 California Institute of Technology 1200 East California Boulevard CA 91125, Pasadena USA ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] cwp and QDEC scale
Hi, I would appreciate if you can help me with the following question: what should be the range values on the QDEC and/or GLM color scale if the cwp values for the cached clusters at thresh 2 and cwpvalthresh .99 are between 0.4465 and 0.9710? Also, I wonder if there is a way in QDEC to extract the data from the Display window without running the simulation option. Many thanks. AK___ 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] Cut plane feature in tksurfer
Dear FreeSurfers, I am following the cut plane steps on the freesurfer wiki (http://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferOccipitalFlattenedPatch). I marked a closed areas, press the 'cut closed line' button, left-click in the area, and then press the 'fill uncut area' button. Upon clicking this last button, tksurfer crashes and the below error appears. tksurfer.bin: tnl/t_vertex.c:407: update_input_ptrs: Assertion `a[j].inputstride == vptr-stride' failed. Abort I've seen two other posts with the same problem (links below), but no solution. Can anyone advise on this? Regards, Jodie http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg14612.html http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg16303.html -- Jodie Davies-Thompson, Postdoctoral Fellow Department of Ophthalmology Visual Sciences UBC/VGH Eye Care Centre 2550 Willow Street Vancouver, BC Canada V5Z 3N9 Tel: 604-875-411 ext 69003 ___ 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] retinotopy analysis description
Dear Freesurfers, I am trying to describe how freesurfer conducts it's retinotopy analysis to make the polar, eccen and fieldsign maps. Is there a detailed description of this somewhere? I can't seem to find an indepth description on the wiki. Thanks. Michelle ___ 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] Table for aparc+aseg
Dear FreeSurfers, In aparc+aseg file, each segmented or parceled region seems to be labeled by its own intensity (e.g. the intensity is 53 in the right hippocampus, 10 in the left thalamus...) when I see it on FSL viewer. Where can I find the table that shows the relationship between the intensity and the name of brain region? I want to extract the specific brain regions (e.g. parahippocampal gyrus, fusiform gyrus...) from the result of aparc+aseg, and use them for the seed mask or the termination mask in structural connectivity analysis (tractography). I appreciate your help. Thank you, Shige ___ 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] Table for aparc+aseg
Hi Shige - See $FREESURFER_HOME/FreeSurferColorLUT.txt. a.y On Fri, 7 Oct 2011, Shigetoshi Takaya wrote: Dear FreeSurfers, In aparc+aseg file, each segmented or parceled region seems to be labeled by its own intensity (e.g. the intensity is 53 in the right hippocampus, 10 in the left thalamus...) when I see it on FSL viewer. Where can I find the table that shows the relationship between the intensity and the name of brain region? I want to extract the specific brain regions (e.g. parahippocampal gyrus, fusiform gyrus...) from the result of aparc+aseg, and use them for the seed mask or the termination mask in structural connectivity analysis (tractography). I appreciate your help. Thank you, Shige ___ 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.
[Freesurfer] What kind of data could be processed by FreeSurfer
I am using recon-all command to process some analyze images. But it seems that this command does not work for all .img images. For example, I have an image with the following information: 256x256x124 0.7mm x 0.7mm x 1.5mm data type: uint8 description: position:000 file orientation: 1 0 0 0 1 0 0 0 1 working orientation: 1 0 0 0 1 0 0 0 1 Will the dimension, resolution, and data type all matter in the process? ___ 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] What kind of data could be processed by FreeSurfer
Hi Jie, it should be ok. We typically don't recommend this type of french fry voxel with one dimension beting almost 4 times as long as the others. You are usually better off getting closer to isotropic. That said, if the SNR is good enough try giving it to recon-all. One thing to be wary of though is the orientation. Do you have a .mat file to go with the .hdr/.img? Otherwise you won't be able to tell left from right. Can you get them in some other format, such as nifti? cheers Bruce On Fri, 7 Oct 2011, Jie Shi wrote: I am using recon-all command to process some analyze images. But it seems that this command does not work for all .img images. For example, I have an image with the following information: 256x256x124 0.7mm x 0.7mm x 1.5mm data type: uint8 description: position:0 0 0 file orientation: 1 0 0 0 1 0 0 0 1 working orientation: 1 0 0 0 1 0 0 0 1 Will the dimension, resolution, and data type all matter in the process? ___ 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] normalised functional volumetric data to fsaverage
Hi All, I have some functional beta maps normalised to the T1 template using spm8 and I am wondering how to map them onto the fsaverage surface ? In native subject space, I pipe a functional scout image into bbregister to get a registration matrix which is then used to map volumetric beta maps to native freesurfer surface and fsaverage surface. How do I do this with the normalised functional data ? Thanks Ri ___ 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] warped flat occip patches and fieldsign maps
Hi Bruce, I've uploaded a tar file called umali_fieldsign_swirl. It contains two directories one anatomical and the other retinotopy both from the same subject 29: ld29 which contains the recon-all output anatomical data sj29 which contains all the retinotopy data. the subjectfilename says ld29 The fieldsign map on the flattened patch has some out-of-plane swirls. Is it from incorrect cuts or something else? Thanks. Michelle On Fri, Oct 7, 2011 at 8:32 AM, Bruce Fischl fis...@nmr.mgh.harvard.eduwrote: Hi Michelle, the odd shaped shards and triangles usually means you recreated the surfaces after flattening, so the flattening needs to be redone. The swirls can be a number of things, possibly incorrect cuts. If you want to upload an example I'll take a look. cheers Bruce On Thu, 6 Oct 2011, Michelle Umali wrote: Dear freesurfers, I've been analyzing my retinotopy , have finally been able to run fieldsign-sess without running into dimension mismatch errors. Everything seemed ok until I tried looking at the fieldsign maps on flat patches. Some patches are warped with odd out of plane swirls. In others, all i get are odd shaped shards and triangles. What might be the cause? thanks, Michelle 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/**compliancelinehttp://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@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] normalised functional volumetric data to fsaverage
Hi Ri if you have them on the surface using the bbregister registration you can use mri_surf2surf to map them to fsaverage (or any other subject). cheers Bruce On Fri, 7 Oct 2011, Ritobrato Datta wrote: Hi All, I have some functional beta maps normalised to the T1 template using spm8 and I am wondering how to map them onto the fsaverage surface ? In native subject space, I pipe a functional scout image into bbregister to get a registration matrix which is then used to map volumetric beta maps to native freesurfer surface and fsaverage surface. How do I do this with the normalised functional data ? Thanks Ri ___ 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.
